diff --git a/Makefile b/Makefile index dfc23e1c36..b48cb80029 100644 --- a/Makefile +++ b/Makefile @@ -21,10 +21,11 @@ SHEET_ID = $(shell ${SHELL} ./utils/get-value.sh google_sheet_id) SHEET_TABS = $(shell ${SHELL} ./utils/get-value.sh google_sheet_tabs) SHEET_MODULE_PATH = $(SOURCE_SCHEMA_DIR)/$(SHEET_MODULE).yaml -# environment variables -include config.env +## environment variables +#include config.env -GEN_PARGS = +# MAM 2023-10-06 hard-coding exclude statements +GEN_PARGS = --exclude excel --exclude graphql --exclude prefixmap --exclude protobuf --exclude shacl --exclude shex --exclude markdown ifdef LINKML_GENERATORS_PROJECT_ARGS GEN_PARGS = ${LINKML_GENERATORS_PROJECT_ARGS} endif @@ -187,4 +188,4 @@ clean: rm -fr docs/* rm -fr $(PYMODEL)/* -include project.Makefile +include project.Makefile \ No newline at end of file diff --git a/about.yaml b/about.yaml index be43f65af5..9584a530f2 100644 --- a/about.yaml +++ b/about.yaml @@ -1,7 +1,7 @@ --- name: mixs_6_2_for_merge author: Mark Andrew Miller -description: MIxS: the Minimum Information about any (X) Sequence standard +description: "MIxS: the Minimum Information about any (X) Sequence standard" source_schema_path: src/mixs_6_2_for_merge/schema/mixs_6_2_for_merge.yaml -google_sheet_id: 1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ -google_sheet_tabs: personinfo enums +#google_sheet_id: 1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ +#google_sheet_tabs: personinfo enums diff --git a/src/mixs_6_2_for_merge/schema/mixs_6_2_for_merge.yaml b/src/mixs_6_2_for_merge/schema/mixs_6_2_for_merge.yaml index 6e31ee8e2e..97ae82aef0 100644 --- a/src/mixs_6_2_for_merge/schema/mixs_6_2_for_merge.yaml +++ b/src/mixs_6_2_for_merge/schema/mixs_6_2_for_merge.yaml @@ -2444,37 +2444,171 @@ enums: other: text: other slots: - migs_eu_data: - name: migs_eu_data - description: Data that complies with checklist MigsEu - title: MigsEu data + migs_ba_data: + name: migs_ba_data + description: Data that complies with checklist MigsBa + title: MigsBa data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:migs_eu_data + slot_uri: MIXS:migs_ba_data multivalued: true - range: MigsEu + range: MigsBa inlined: true inlined_as_list: true - plant_associated_data: - name: plant_associated_data - description: Data that complies with Extension PlantAssociated - title: PlantAssociated data + agriculture_data: + name: agriculture_data + description: Data that complies with Extension Agriculture + title: Agriculture data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:plant_associated_data + slot_uri: MIXS:agriculture_data multivalued: true - range: PlantAssociated + range: Agriculture inlined: true inlined_as_list: true - migs_eu_plant_associated_data: - name: migs_eu_plant_associated_data - description: Data that complies with MigsEu combined with PlantAssociated - title: MigsEuPlantAssociated data + migs_ba_agriculture_data: + name: migs_ba_agriculture_data + description: Data that complies with MigsBa combined with Agriculture + title: MigsBaAgriculture data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:migs_eu_plant_associated_data + slot_uri: MIXS:migs_ba_agriculture_data multivalued: true - range: MigsEuPlantAssociated + range: MigsBaAgriculture + inlined: true + inlined_as_list: true + air_data: + name: air_data + description: Data that complies with Extension Air + title: Air data + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - air + domain: MixsCompliantData + slot_uri: MIXS:air_data + multivalued: true + range: Air + inlined: true + inlined_as_list: true + migs_ba_air_data: + name: migs_ba_air_data + description: Data that complies with MigsBa combined with Air + title: MigsBaAir data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:migs_ba_air_data + multivalued: true + range: MigsBaAir + inlined: true + inlined_as_list: true + built_environment_data: + name: built_environment_data + description: Data that complies with Extension BuiltEnvironment + title: BuiltEnvironment data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:built_environment_data + multivalued: true + range: BuiltEnvironment + inlined: true + inlined_as_list: true + migs_ba_built_environment_data: + name: migs_ba_built_environment_data + description: Data that complies with MigsBa combined with BuiltEnvironment + title: MigsBaBuiltEnvironment data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:migs_ba_built_environment_data + multivalued: true + range: MigsBaBuiltEnvironment + inlined: true + inlined_as_list: true + food_animal_and_animal_feed_data: + name: food_animal_and_animal_feed_data + description: Data that complies with Extension FoodAnimalAndAnimalFeed + title: FoodAnimalAndAnimalFeed data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:food_animal_and_animal_feed_data + multivalued: true + range: FoodAnimalAndAnimalFeed + inlined: true + inlined_as_list: true + migs_ba_food_animal_and_animal_feed_data: + name: migs_ba_food_animal_and_animal_feed_data + description: Data that complies with MigsBa combined with FoodAnimalAndAnimalFeed + title: MigsBaFoodAnimalAndAnimalFeed data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:migs_ba_food_animal_and_animal_feed_data + multivalued: true + range: MigsBaFoodAnimalAndAnimalFeed + inlined: true + inlined_as_list: true + food_farm_environment_data: + name: food_farm_environment_data + description: Data that complies with Extension FoodFarmEnvironment + title: FoodFarmEnvironment data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:food_farm_environment_data + multivalued: true + range: FoodFarmEnvironment + inlined: true + inlined_as_list: true + migs_ba_food_farm_environment_data: + name: migs_ba_food_farm_environment_data + description: Data that complies with MigsBa combined with FoodFarmEnvironment + title: MigsBaFoodFarmEnvironment data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:migs_ba_food_farm_environment_data + multivalued: true + range: MigsBaFoodFarmEnvironment + inlined: true + inlined_as_list: true + food_food_production_facility_data: + name: food_food_production_facility_data + description: Data that complies with Extension FoodFoodProductionFacility + title: FoodFoodProductionFacility data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:food_food_production_facility_data + multivalued: true + range: FoodFoodProductionFacility + inlined: true + inlined_as_list: true + migs_ba_food_food_production_facility_data: + name: migs_ba_food_food_production_facility_data + description: Data that complies with MigsBa combined with FoodFoodProductionFacility + title: MigsBaFoodFoodProductionFacility data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:migs_ba_food_food_production_facility_data + multivalued: true + range: MigsBaFoodFoodProductionFacility + inlined: true + inlined_as_list: true + food_human_foods_data: + name: food_human_foods_data + description: Data that complies with Extension FoodHumanFoods + title: FoodHumanFoods data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:food_human_foods_data + multivalued: true + range: FoodHumanFoods + inlined: true + inlined_as_list: true + migs_ba_food_human_foods_data: + name: migs_ba_food_human_foods_data + description: Data that complies with MigsBa combined with FoodHumanFoods + title: MigsBaFoodHumanFoods data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:migs_ba_food_human_foods_data + multivalued: true + range: MigsBaFoodHumanFoods inlined: true inlined_as_list: true host_associated_data: @@ -2488,15 +2622,15 @@ slots: range: HostAssociated inlined: true inlined_as_list: true - migs_eu_host_associated_data: - name: migs_eu_host_associated_data - description: Data that complies with MigsEu combined with HostAssociated - title: MigsEuHostAssociated data + migs_ba_host_associated_data: + name: migs_ba_host_associated_data + description: Data that complies with MigsBa combined with HostAssociated + title: MigsBaHostAssociated data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:migs_eu_host_associated_data + slot_uri: MIXS:migs_ba_host_associated_data multivalued: true - range: MigsEuHostAssociated + range: MigsBaHostAssociated inlined: true inlined_as_list: true human_associated_data: @@ -2510,15 +2644,15 @@ slots: range: HumanAssociated inlined: true inlined_as_list: true - migs_eu_human_associated_data: - name: migs_eu_human_associated_data - description: Data that complies with MigsEu combined with HumanAssociated - title: MigsEuHumanAssociated data + migs_ba_human_associated_data: + name: migs_ba_human_associated_data + description: Data that complies with MigsBa combined with HumanAssociated + title: MigsBaHumanAssociated data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:migs_eu_human_associated_data + slot_uri: MIXS:migs_ba_human_associated_data multivalued: true - range: MigsEuHumanAssociated + range: MigsBaHumanAssociated inlined: true inlined_as_list: true human_gut_data: @@ -2532,15 +2666,15 @@ slots: range: HumanGut inlined: true inlined_as_list: true - migs_eu_human_gut_data: - name: migs_eu_human_gut_data - description: Data that complies with MigsEu combined with HumanGut - title: MigsEuHumanGut data + migs_ba_human_gut_data: + name: migs_ba_human_gut_data + description: Data that complies with MigsBa combined with HumanGut + title: MigsBaHumanGut data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:migs_eu_human_gut_data + slot_uri: MIXS:migs_ba_human_gut_data multivalued: true - range: MigsEuHumanGut + range: MigsBaHumanGut inlined: true inlined_as_list: true human_oral_data: @@ -2554,5245 +2688,3434 @@ slots: range: HumanOral inlined: true inlined_as_list: true - migs_eu_human_oral_data: - name: migs_eu_human_oral_data - description: Data that complies with MigsEu combined with HumanOral - title: MigsEuHumanOral data + migs_ba_human_oral_data: + name: migs_ba_human_oral_data + description: Data that complies with MigsBa combined with HumanOral + title: MigsBaHumanOral data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:migs_eu_human_oral_data + slot_uri: MIXS:migs_ba_human_oral_data multivalued: true - range: MigsEuHumanOral + range: MigsBaHumanOral inlined: true inlined_as_list: true - soil_data: - name: soil_data - description: Data that complies with Extension Soil - title: Soil data + human_skin_data: + name: human_skin_data + description: Data that complies with Extension HumanSkin + title: HumanSkin data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - soil domain: MixsCompliantData - slot_uri: MIXS:soil_data + slot_uri: MIXS:human_skin_data multivalued: true - range: Soil + range: HumanSkin inlined: true inlined_as_list: true - migs_eu_soil_data: - name: migs_eu_soil_data - description: Data that complies with MigsEu combined with Soil - title: MigsEuSoil data + migs_ba_human_skin_data: + name: migs_ba_human_skin_data + description: Data that complies with MigsBa combined with HumanSkin + title: MigsBaHumanSkin data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:migs_eu_soil_data + slot_uri: MIXS:migs_ba_human_skin_data multivalued: true - range: MigsEuSoil + range: MigsBaHumanSkin inlined: true inlined_as_list: true - water_data: - name: water_data - description: Data that complies with Extension Water - title: Water data + human_vaginal_data: + name: human_vaginal_data + description: Data that complies with Extension HumanVaginal + title: HumanVaginal data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - water domain: MixsCompliantData - slot_uri: MIXS:water_data + slot_uri: MIXS:human_vaginal_data multivalued: true - range: Water + range: HumanVaginal inlined: true inlined_as_list: true - migs_eu_water_data: - name: migs_eu_water_data - description: Data that complies with MigsEu combined with Water - title: MigsEuWater data + migs_ba_human_vaginal_data: + name: migs_ba_human_vaginal_data + description: Data that complies with MigsBa combined with HumanVaginal + title: MigsBaHumanVaginal data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:migs_eu_water_data + slot_uri: MIXS:migs_ba_human_vaginal_data multivalued: true - range: MigsEuWater + range: MigsBaHumanVaginal inlined: true inlined_as_list: true - mims_data: - name: mims_data - description: Data that complies with checklist Mims - title: Mims data + hydrocarbon_resources_cores_data: + name: hydrocarbon_resources_cores_data + description: Data that complies with Extension HydrocarbonResourcesCores + title: HydrocarbonResourcesCores data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:mims_data + slot_uri: MIXS:hydrocarbon_resources_cores_data multivalued: true - range: Mims + range: HydrocarbonResourcesCores inlined: true inlined_as_list: true - mims_plant_associated_data: - name: mims_plant_associated_data - description: Data that complies with Mims combined with PlantAssociated - title: MimsPlantAssociated data + migs_ba_hydrocarbon_resources_cores_data: + name: migs_ba_hydrocarbon_resources_cores_data + description: Data that complies with MigsBa combined with HydrocarbonResourcesCores + title: MigsBaHydrocarbonResourcesCores data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:mims_plant_associated_data + slot_uri: MIXS:migs_ba_hydrocarbon_resources_cores_data multivalued: true - range: MimsPlantAssociated + range: MigsBaHydrocarbonResourcesCores inlined: true inlined_as_list: true - mims_host_associated_data: - name: mims_host_associated_data - description: Data that complies with Mims combined with HostAssociated - title: MimsHostAssociated data + hydrocarbon_resources_fluids_swabs_data: + name: hydrocarbon_resources_fluids_swabs_data + description: Data that complies with Extension HydrocarbonResourcesFluidsSwabs + title: HydrocarbonResourcesFluidsSwabs data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:mims_host_associated_data + slot_uri: MIXS:hydrocarbon_resources_fluids_swabs_data multivalued: true - range: MimsHostAssociated + range: HydrocarbonResourcesFluidsSwabs inlined: true inlined_as_list: true - mims_human_associated_data: - name: mims_human_associated_data - description: Data that complies with Mims combined with HumanAssociated - title: MimsHumanAssociated data + migs_ba_hydrocarbon_resources_fluids_swabs_data: + name: migs_ba_hydrocarbon_resources_fluids_swabs_data + description: Data that complies with MigsBa combined with HydrocarbonResourcesFluidsSwabs + title: MigsBaHydrocarbonResourcesFluidsSwabs data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:mims_human_associated_data + slot_uri: MIXS:migs_ba_hydrocarbon_resources_fluids_swabs_data multivalued: true - range: MimsHumanAssociated + range: MigsBaHydrocarbonResourcesFluidsSwabs inlined: true inlined_as_list: true - mims_human_gut_data: - name: mims_human_gut_data - description: Data that complies with Mims combined with HumanGut - title: MimsHumanGut data + microbial_mat_biofilm_data: + name: microbial_mat_biofilm_data + description: Data that complies with Extension MicrobialMatBiofilm + title: MicrobialMatBiofilm data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:mims_human_gut_data + slot_uri: MIXS:microbial_mat_biofilm_data multivalued: true - range: MimsHumanGut + range: MicrobialMatBiofilm inlined: true inlined_as_list: true - mims_human_oral_data: - name: mims_human_oral_data - description: Data that complies with Mims combined with HumanOral - title: MimsHumanOral data + migs_ba_microbial_mat_biofilm_data: + name: migs_ba_microbial_mat_biofilm_data + description: Data that complies with MigsBa combined with MicrobialMatBiofilm + title: MigsBaMicrobialMatBiofilm data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:mims_human_oral_data + slot_uri: MIXS:migs_ba_microbial_mat_biofilm_data multivalued: true - range: MimsHumanOral + range: MigsBaMicrobialMatBiofilm inlined: true inlined_as_list: true - mims_soil_data: - name: mims_soil_data - description: Data that complies with Mims combined with Soil - title: MimsSoil data + miscellaneous_natural_or_artificial_environment_data: + name: miscellaneous_natural_or_artificial_environment_data + description: Data that complies with Extension MiscellaneousNaturalOrArtificialEnvironment + title: MiscellaneousNaturalOrArtificialEnvironment data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:mims_soil_data + slot_uri: MIXS:miscellaneous_natural_or_artificial_environment_data multivalued: true - range: MimsSoil + range: MiscellaneousNaturalOrArtificialEnvironment inlined: true inlined_as_list: true - mims_water_data: - name: mims_water_data - description: Data that complies with Mims combined with Water - title: MimsWater data + migs_ba_miscellaneous_natural_or_artificial_environment_data: + name: migs_ba_miscellaneous_natural_or_artificial_environment_data + description: Data that complies with MigsBa combined with MiscellaneousNaturalOrArtificialEnvironment + title: MigsBaMiscellaneousNaturalOrArtificialEnvironment data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:mims_water_data + slot_uri: MIXS:migs_ba_miscellaneous_natural_or_artificial_environment_data multivalued: true - range: MimsWater + range: MigsBaMiscellaneousNaturalOrArtificialEnvironment inlined: true inlined_as_list: true - mimarks_s_data: - name: mimarks_s_data - description: Data that complies with checklist MimarksS - title: MimarksS data + plant_associated_data: + name: plant_associated_data + description: Data that complies with Extension PlantAssociated + title: PlantAssociated data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:mimarks_s_data + slot_uri: MIXS:plant_associated_data multivalued: true - range: MimarksS + range: PlantAssociated inlined: true inlined_as_list: true - mimarks_s_plant_associated_data: - name: mimarks_s_plant_associated_data - description: Data that complies with MimarksS combined with PlantAssociated - title: MimarksSPlantAssociated data + migs_ba_plant_associated_data: + name: migs_ba_plant_associated_data + description: Data that complies with MigsBa combined with PlantAssociated + title: MigsBaPlantAssociated data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:mimarks_s_plant_associated_data + slot_uri: MIXS:migs_ba_plant_associated_data multivalued: true - range: MimarksSPlantAssociated + range: MigsBaPlantAssociated inlined: true inlined_as_list: true - mimarks_s_host_associated_data: - name: mimarks_s_host_associated_data - description: Data that complies with MimarksS combined with HostAssociated - title: MimarksSHostAssociated data + sediment_data: + name: sediment_data + description: Data that complies with Extension Sediment + title: Sediment data from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sediment domain: MixsCompliantData - slot_uri: MIXS:mimarks_s_host_associated_data + slot_uri: MIXS:sediment_data multivalued: true - range: MimarksSHostAssociated + range: Sediment inlined: true inlined_as_list: true - mimarks_s_human_associated_data: - name: mimarks_s_human_associated_data - description: Data that complies with MimarksS combined with HumanAssociated - title: MimarksSHumanAssociated data + migs_ba_sediment_data: + name: migs_ba_sediment_data + description: Data that complies with MigsBa combined with Sediment + title: MigsBaSediment data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:mimarks_s_human_associated_data + slot_uri: MIXS:migs_ba_sediment_data multivalued: true - range: MimarksSHumanAssociated + range: MigsBaSediment inlined: true inlined_as_list: true - mimarks_s_human_gut_data: - name: mimarks_s_human_gut_data - description: Data that complies with MimarksS combined with HumanGut - title: MimarksSHumanGut data + soil_data: + name: soil_data + description: Data that complies with Extension Soil + title: Soil data from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - soil domain: MixsCompliantData - slot_uri: MIXS:mimarks_s_human_gut_data + slot_uri: MIXS:soil_data multivalued: true - range: MimarksSHumanGut + range: Soil inlined: true inlined_as_list: true - mimarks_s_human_oral_data: - name: mimarks_s_human_oral_data - description: Data that complies with MimarksS combined with HumanOral - title: MimarksSHumanOral data + migs_ba_soil_data: + name: migs_ba_soil_data + description: Data that complies with MigsBa combined with Soil + title: MigsBaSoil data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:mimarks_s_human_oral_data + slot_uri: MIXS:migs_ba_soil_data multivalued: true - range: MimarksSHumanOral + range: MigsBaSoil inlined: true inlined_as_list: true - mimarks_s_soil_data: - name: mimarks_s_soil_data - description: Data that complies with MimarksS combined with Soil - title: MimarksSSoil data + symbiont_associated_data: + name: symbiont_associated_data + description: Data that complies with Extension SymbiontAssociated + title: SymbiontAssociated data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:mimarks_s_soil_data + slot_uri: MIXS:symbiont_associated_data multivalued: true - range: MimarksSSoil + range: SymbiontAssociated inlined: true inlined_as_list: true - mimarks_s_water_data: - name: mimarks_s_water_data - description: Data that complies with MimarksS combined with Water - title: MimarksSWater data + migs_ba_symbiont_associated_data: + name: migs_ba_symbiont_associated_data + description: Data that complies with MigsBa combined with SymbiontAssociated + title: MigsBaSymbiontAssociated data from_schema: https://w3id.org/mixs-6-2-rc domain: MixsCompliantData - slot_uri: MIXS:mimarks_s_water_data + slot_uri: MIXS:migs_ba_symbiont_associated_data multivalued: true - range: MimarksSWater + range: MigsBaSymbiontAssociated inlined: true inlined_as_list: true - HACCP_term: - name: HACCP_term - description: Hazard Analysis Critical Control Points (HACCP) food safety terms; - This field accepts terms listed under HACCP guide food safety term (http://purl.obolibrary.org/obo/FOODON_03530221) - title: Hazard Analysis Critical Control Points (HACCP) guide food safety term - examples: - - value: tetrodotoxic poisoning [FOODON:03530249] + wastewater_sludge_data: + name: wastewater_sludge_data + description: Data that complies with Extension WastewaterSludge + title: WastewaterSludge data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - food - - term - slot_uri: MIXS:0001215 + domain: MixsCompliantData + slot_uri: MIXS:wastewater_sludge_data multivalued: true - range: string - required: false - recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ - structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ - interpolated: true - partial_match: true - IFSAC_category: - name: IFSAC_category - annotations: - Expected_value: - tag: Expected_value - value: IFSAC term - description: 'The IFSAC food categorization scheme has five distinct levels to - which foods can be assigned, depending upon the type of food. First, foods are - assigned to one of four food groups (aquatic animals, land animals, plants, - and other). Food groups include increasingly specific food categories; dairy, - eggs, meat and poultry, and game are in the land animal food group, and the - category meat and poultry is further subdivided into more specific categories - of meat (beef, pork, other meat) and poultry (chicken, turkey, other poultry). - Finally, foods are differentiated by differences in food processing (such as - pasteurized fluid dairy products, unpasteurized fluid dairy products, pasteurized - solid and semi-solid dairy products, and unpasteurized solid and semi-solid - dairy products. An IFSAC food category chart is available from https://www.cdc.gov/foodsafety/ifsac/projects/food-categorization-scheme.html - PMID: 28926300' - title: Interagency Food Safety Analytics Collaboration (IFSAC) category - examples: - - value: Plants:Produce:Vegetables:Herbs:Dried Herbs + range: WastewaterSludge + inlined: true + inlined_as_list: true + migs_ba_wastewater_sludge_data: + name: migs_ba_wastewater_sludge_data + description: Data that complies with MigsBa combined with WastewaterSludge + title: MigsBaWastewaterSludge data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - food - string_serialization: '{text}' - slot_uri: MIXS:0001179 + domain: MixsCompliantData + slot_uri: MIXS:migs_ba_wastewater_sludge_data multivalued: true - required: true - abs_air_humidity: - name: abs_air_humidity - annotations: - Preferred_unit: - tag: Preferred_unit - value: gram per gram, kilogram per kilogram, kilogram, pound - description: Actual mass of water vapor - mh20 - present in the air water vapor - mixture - title: absolute air humidity - examples: - - value: 9 gram per gram + range: MigsBaWastewaterSludge + inlined: true + inlined_as_list: true + water_data: + name: water_data + description: Data that complies with Extension Water + title: Water data from_schema: https://w3id.org/mixs-6-2-rc keywords: - - absolute - - air - - humidity - slot_uri: MIXS:0000122 - multivalued: false - range: string - required: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - adapters: - name: adapters - annotations: - Expected_value: - tag: Expected_value - value: adapter A and B sequence - description: Adapters provide priming sequences for both amplification and sequencing - of the sample-library fragments. Both adapters should be reported; in uppercase - letters - title: adapters - examples: - - value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT - in_subset: - - sequencing - from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{dna};{dna}' - slot_uri: MIXS:0000048 - multivalued: false - add_recov_method: - name: add_recov_method - annotations: - Expected_value: - tag: Expected_value - value: enumeration;timestamp - description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed - for increase of hydrocarbon recovery from resource and start date for each one - of them. If "other" is specified, please propose entry in "additional info" - field - title: secondary and tertiary recovery methods and start date - examples: - - value: Polymer Addition;2018-06-21T14:30Z + - water + domain: MixsCompliantData + slot_uri: MIXS:water_data + multivalued: true + range: Water + inlined: true + inlined_as_list: true + migs_ba_water_data: + name: migs_ba_water_data + description: Data that complies with MigsBa combined with Water + title: MigsBaWater data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - date - - method - - recover - - secondary - - start - string_serialization: '[Water Injection|Dump Flood|Gas Injection|Wag Immiscible - Injection|Polymer Addition|Surfactant Addition|Not Applicable|other];{timestamp}' - slot_uri: MIXS:0001009 - multivalued: false - required: true - additional_info: - name: additional_info - description: Information that doesn't fit anywhere else. Can also be used to propose - new entries for fields with controlled vocabulary - title: additional info + domain: MixsCompliantData + slot_uri: MIXS:migs_ba_water_data + multivalued: true + range: MigsBaWater + inlined: true + inlined_as_list: true + migs_eu_data: + name: migs_eu_data + description: Data that complies with checklist MigsEu + title: MigsEu data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - information - slot_uri: MIXS:0000300 - multivalued: false - range: string - required: false - recommended: false - address: - name: address - annotations: - Expected_value: - tag: Expected_value - value: value - description: The street name and building number where the sampling occurred - title: address + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_data + multivalued: true + range: MigsEu + inlined: true + inlined_as_list: true + migs_eu_agriculture_data: + name: migs_eu_agriculture_data + description: Data that complies with MigsEu combined with Agriculture + title: MigsEuAgriculture data from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{integer}{text}' - slot_uri: MIXS:0000218 - multivalued: false - required: false - recommended: false - adj_room: - name: adj_room - description: List of rooms (room number, room name) immediately adjacent to the - sampling room - title: adjacent rooms + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_agriculture_data + multivalued: true + range: MigsEuAgriculture + inlined: true + inlined_as_list: true + migs_eu_air_data: + name: migs_eu_air_data + description: Data that complies with MigsEu combined with Air + title: MigsEuAir data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - adjacent - - room - slot_uri: MIXS:0000219 - multivalued: false - range: string - required: false - recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ - structured_pattern: - syntax: ^{room_name};{room_number}$ - interpolated: true - partial_match: true - adjacent_environment: - name: adjacent_environment - annotations: - Expected_value: - tag: Expected_value - value: ENVO_01001110 or ENVO_00000070 - description: Description of the environmental system or features that are adjacent - to the sampling site. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) - and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple - terms can be separated by pipes - title: environment adjacent to site - examples: - - value: estuarine biome [ENVO:01000020] + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_air_data + multivalued: true + range: MigsEuAir + inlined: true + inlined_as_list: true + migs_eu_built_environment_data: + name: migs_eu_built_environment_data + description: Data that complies with MigsEu combined with BuiltEnvironment + title: MigsEuBuiltEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - adjacent - - environment - - site - string_serialization: '{termLabel}{[termID]}' - slot_uri: MIXS:0001121 + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_built_environment_data multivalued: true - required: false - recommended: false - aero_struc: - name: aero_struc - description: Aerospace structures typically consist of thin plates with stiffeners - for the external surfaces, bulkheads and frames to support the shape and fasteners - such as welds, rivets, screws and bolts to hold the components together - title: aerospace structure - examples: - - value: plane + range: MigsEuBuiltEnvironment + inlined: true + inlined_as_list: true + migs_eu_food_animal_and_animal_feed_data: + name: migs_eu_food_animal_and_animal_feed_data + description: Data that complies with MigsEu combined with FoodAnimalAndAnimalFeed + title: MigsEuFoodAnimalAndAnimalFeed data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000773 - multivalued: false - range: AERO_STRUC_ENUM - required: false - recommended: false - agrochem_addition: - name: agrochem_addition - annotations: - Expected_value: - tag: Expected_value - value: agrochemical name;agrochemical amount;timestamp - Preferred_unit: - tag: Preferred_unit - value: gram, mole per liter, milligram per liter - description: Addition of fertilizers, pesticides, etc. - amount and time of applications - title: history/agrochemical additions - examples: - - value: roundup;5 milligram per liter;2018-06-21 + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_food_animal_and_animal_feed_data + multivalued: true + range: MigsEuFoodAnimalAndAnimalFeed + inlined: true + inlined_as_list: true + migs_eu_food_farm_environment_data: + name: migs_eu_food_farm_environment_data + description: Data that complies with MigsEu combined with FoodFarmEnvironment + title: MigsEuFoodFarmEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - history - string_serialization: '{text};{float} {unit};{timestamp}' - slot_uri: MIXS:0000639 + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_food_farm_environment_data multivalued: true - required: false - recommended: false - air_PM_concen: - name: air_PM_concen - annotations: - Expected_value: - tag: Expected_value - value: particulate matter name;measurement value - description: Concentration of substances that remain suspended in the air, and - comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can - report multiple PM's by entering numeric values preceded by name of PM - title: air particulate matter concentration - examples: - - value: PM2.5;10 microgram per cubic meter + range: MigsEuFoodFarmEnvironment + inlined: true + inlined_as_list: true + migs_eu_food_food_production_facility_data: + name: migs_eu_food_food_production_facility_data + description: Data that complies with MigsEu combined with FoodFoodProductionFacility + title: MigsEuFoodFoodProductionFacility data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - air - - concentration - - particle - - particulate - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000108 + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_food_food_production_facility_data multivalued: true - required: false - recommended: false - air_flow_impede: - name: air_flow_impede - annotations: - Expected_value: - tag: Expected_value - value: enumeration;obstruction type; distance from sampling device - description: Presence of objects in the area that would influence or impede air - flow through the air filter - title: local air flow impediments - examples: - - value: obstructed;hay bales; 2 m + range: MigsEuFoodFoodProductionFacility + inlined: true + inlined_as_list: true + migs_eu_food_human_foods_data: + name: migs_eu_food_human_foods_data + description: Data that complies with MigsEu combined with FoodHumanFoods + title: MigsEuFoodHumanFoods data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - air - string_serialization: '[obstructed|unobstructed]; {text}; {measurement value}' - slot_uri: MIXS:0001146 + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_food_human_foods_data multivalued: true - required: false - recommended: false - air_temp: - name: air_temp - annotations: - Preferred_unit: - tag: Preferred_unit - value: degree Celsius - description: Temperature of the air at the time of sampling - title: air temperature + range: MigsEuFoodHumanFoods + inlined: true + inlined_as_list: true + migs_eu_host_associated_data: + name: migs_eu_host_associated_data + description: Data that complies with MigsEu combined with HostAssociated + title: MigsEuHostAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - air - - temperature - slot_uri: MIXS:0000124 - multivalued: false - range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - air_temp_regm: - name: air_temp_regm - annotations: - Expected_value: - tag: Expected_value - value: temperature value;treatment interval and duration - Preferred_unit: - tag: Preferred_unit - value: meter - description: Information about treatment involving an exposure to varying temperatures; - should include the temperature, treatment regimen including how many times the - treatment was repeated, how long each treatment lasted, and the start and end - time of the entire treatment; can include different temperature regimens - title: air temperature regimen - examples: - - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_host_associated_data + multivalued: true + range: MigsEuHostAssociated + inlined: true + inlined_as_list: true + migs_eu_human_associated_data: + name: migs_eu_human_associated_data + description: Data that complies with MigsEu combined with HumanAssociated + title: MigsEuHumanAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - air - - regimen - - temperature - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000551 + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_human_associated_data multivalued: true - required: false - recommended: false - al_sat: - name: al_sat - annotations: - Preferred_unit: - tag: Preferred_unit - value: percentage - description: Aluminum saturation (esp. For tropical soils) - title: extreme_unusual_properties/Al saturation + range: MigsEuHumanAssociated + inlined: true + inlined_as_list: true + migs_eu_human_gut_data: + name: migs_eu_human_gut_data + description: Data that complies with MigsEu combined with HumanGut + title: MigsEuHumanGut data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - extreme - - properties - - saturation - - unusual - slot_uri: MIXS:0000607 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - al_sat_meth: - name: al_sat_meth - description: Reference or method used in determining Al saturation - title: extreme_unusual_properties/Al saturation method + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_human_gut_data + multivalued: true + range: MigsEuHumanGut + inlined: true + inlined_as_list: true + migs_eu_human_oral_data: + name: migs_eu_human_oral_data + description: Data that complies with MigsEu combined with HumanOral + title: MigsEuHumanOral data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - extreme - - method - - properties - - saturation - - unusual - slot_uri: MIXS:0000324 - multivalued: false - range: string - required: false - recommended: false - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ - structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ - interpolated: true - partial_match: true - alkalinity: - name: alkalinity - annotations: - Preferred_unit: - tag: Preferred_unit - value: milliequivalent per liter, milligram per liter - description: Alkalinity, the ability of a solution to neutralize acids to the - equivalence point of carbonate or bicarbonate - title: alkalinity - examples: - - value: 50 milligram per liter + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_human_oral_data + multivalued: true + range: MigsEuHumanOral + inlined: true + inlined_as_list: true + migs_eu_human_skin_data: + name: migs_eu_human_skin_data + description: Data that complies with MigsEu combined with HumanSkin + title: MigsEuHumanSkin data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - alkalinity - slot_uri: MIXS:0000421 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - alkalinity_method: - name: alkalinity_method - description: Method used for alkalinity measurement - title: alkalinity method - examples: - - value: titration + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_human_skin_data + multivalued: true + range: MigsEuHumanSkin + inlined: true + inlined_as_list: true + migs_eu_human_vaginal_data: + name: migs_eu_human_vaginal_data + description: Data that complies with MigsEu combined with HumanVaginal + title: MigsEuHumanVaginal data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - alkalinity - - method - slot_uri: MIXS:0000298 - multivalued: false - range: string - required: false - recommended: false - alkyl_diethers: - name: alkyl_diethers - description: Concentration of alkyl diethers - title: alkyl diethers - examples: - - value: 0.005 mole per liter + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_human_vaginal_data + multivalued: true + range: MigsEuHumanVaginal + inlined: true + inlined_as_list: true + migs_eu_hydrocarbon_resources_cores_data: + name: migs_eu_hydrocarbon_resources_cores_data + description: Data that complies with MigsEu combined with HydrocarbonResourcesCores + title: MigsEuHydrocarbonResourcesCores data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000490 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - alt: - name: alt - annotations: - Preferred_unit: - tag: Preferred_unit - value: meter - description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric - balloons and heights of places such as atmospheric layers and clouds. It is - used to measure the height of an object which is above the earth's surface. - In this context, the altitude measurement is the vertical distance between the - earth's surface above sea level and the sampled position in the air - title: altitude - examples: - - value: 100 meter - in_subset: - - environment + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_hydrocarbon_resources_cores_data + multivalued: true + range: MigsEuHydrocarbonResourcesCores + inlined: true + inlined_as_list: true + migs_eu_hydrocarbon_resources_fluids_swabs_data: + name: migs_eu_hydrocarbon_resources_fluids_swabs_data + description: Data that complies with MigsEu combined with HydrocarbonResourcesFluidsSwabs + title: MigsEuHydrocarbonResourcesFluidsSwabs data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000094 - multivalued: false - range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - aminopept_act: - name: aminopept_act - annotations: - Preferred_unit: - tag: Preferred_unit - value: mole per liter per hour - description: Measurement of aminopeptidase activity - title: aminopeptidase activity - examples: - - value: 0.269 mole per liter per hour + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_hydrocarbon_resources_fluids_swabs_data + multivalued: true + range: MigsEuHydrocarbonResourcesFluidsSwabs + inlined: true + inlined_as_list: true + migs_eu_microbial_mat_biofilm_data: + name: migs_eu_microbial_mat_biofilm_data + description: Data that complies with MigsEu combined with MicrobialMatBiofilm + title: MigsEuMicrobialMatBiofilm data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000172 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - ammonium: - name: ammonium - annotations: - Preferred_unit: - tag: Preferred_unit - value: micromole per liter, milligram per liter, parts per million - description: Concentration of ammonium in the sample - title: ammonium - examples: - - value: 1.5 milligram per liter + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_microbial_mat_biofilm_data + multivalued: true + range: MigsEuMicrobialMatBiofilm + inlined: true + inlined_as_list: true + migs_eu_miscellaneous_natural_or_artificial_environment_data: + name: migs_eu_miscellaneous_natural_or_artificial_environment_data + description: Data that complies with MigsEu combined with MiscellaneousNaturalOrArtificialEnvironment + title: MigsEuMiscellaneousNaturalOrArtificialEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000427 - multivalued: false - range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - amniotic_fluid_color: - name: amniotic_fluid_color - description: Specification of the color of the amniotic fluid sample - title: amniotic fluid/color + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_miscellaneous_natural_or_artificial_environment_data + multivalued: true + range: MigsEuMiscellaneousNaturalOrArtificialEnvironment + inlined: true + inlined_as_list: true + migs_eu_plant_associated_data: + name: migs_eu_plant_associated_data + description: Data that complies with MigsEu combined with PlantAssociated + title: MigsEuPlantAssociated data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000276 - multivalued: false - range: string - required: false - recommended: false - amount_light: - name: amount_light - annotations: - Preferred_unit: - tag: Preferred_unit - value: lux, lumens per square meter - description: The unit of illuminance and luminous emittance, measuring luminous - flux per unit area - title: amount of light + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_plant_associated_data + multivalued: true + range: MigsEuPlantAssociated + inlined: true + inlined_as_list: true + migs_eu_sediment_data: + name: migs_eu_sediment_data + description: Data that complies with MigsEu combined with Sediment + title: MigsEuSediment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - light - slot_uri: MIXS:0000140 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - ances_data: - name: ances_data - description: Information about either pedigree or other ancestral information - description (e.g. parental variety in case of mutant or selection), e.g. A/3*B - (meaning [(A x B) x B] x B) - title: ancestral data - examples: - - value: A/3*B + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_sediment_data + multivalued: true + range: MigsEuSediment + inlined: true + inlined_as_list: true + migs_eu_soil_data: + name: migs_eu_soil_data + description: Data that complies with MigsEu combined with Soil + title: MigsEuSoil data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000247 - multivalued: false - range: string - required: false - recommended: false - anim_water_method: - name: anim_water_method - description: Description of the equipment or method used to distribute water to - livestock. This field accepts termed listed under water delivery equipment (http://opendata.inra.fr/EOL/EOL_0001653). - Multiple terms can be separated by pipes - title: animal water delivery method - examples: - - value: water trough [EOL:0001618] + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_soil_data + multivalued: true + range: MigsEuSoil + inlined: true + inlined_as_list: true + migs_eu_symbiont_associated_data: + name: migs_eu_symbiont_associated_data + description: Data that complies with MigsEu combined with SymbiontAssociated + title: MigsEuSymbiontAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - animal - - delivery - - method - - water - slot_uri: MIXS:0001115 + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_symbiont_associated_data multivalued: true - range: string - required: false - recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ - structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ - interpolated: true - partial_match: true - animal_am: - name: animal_am - description: The name(s) (generic or brand) of the antimicrobial(s) given to the - food animal within the last 30 days - title: food animal antimicrobial - examples: - - value: tetracycline + range: MigsEuSymbiontAssociated + inlined: true + inlined_as_list: true + migs_eu_wastewater_sludge_data: + name: migs_eu_wastewater_sludge_data + description: Data that complies with MigsEu combined with WastewaterSludge + title: MigsEuWastewaterSludge data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - animal - - antimicrobial - - food - slot_uri: MIXS:0001243 - multivalued: false - range: string - required: false - recommended: false - animal_am_dur: - name: animal_am_dur - annotations: - Expected_value: - tag: Expected_value - value: value - description: The duration of time (days) that the antimicrobial was administered - to the food animal - title: food animal antimicrobial duration - examples: - - value: 3 days + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_wastewater_sludge_data + multivalued: true + range: MigsEuWastewaterSludge + inlined: true + inlined_as_list: true + migs_eu_water_data: + name: migs_eu_water_data + description: Data that complies with MigsEu combined with Water + title: MigsEuWater data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - animal - - antimicrobial - - duration - - food - - period - string_serialization: '{float} {day}' - slot_uri: MIXS:0001244 - multivalued: false - required: false - recommended: false - animal_am_freq: - name: animal_am_freq - description: The frequency per day that the antimicrobial was adminstered to the - food animal - title: food animal antimicrobial frequency - examples: - - value: '1.5' + domain: MixsCompliantData + slot_uri: MIXS:migs_eu_water_data + multivalued: true + range: MigsEuWater + inlined: true + inlined_as_list: true + migs_org_data: + name: migs_org_data + description: Data that complies with checklist MigsOrg + title: MigsOrg data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - animal - - antimicrobial - - food - - frequency - slot_uri: MIXS:0001245 - range: float - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - animal_am_route: - name: animal_am_route - description: The route by which the antimicrobial is adminstered into the body - of the food animal - title: food animal antimicrobial route of administration - examples: - - value: oral-feed + domain: MixsCompliantData + slot_uri: MIXS:migs_org_data + multivalued: true + range: MigsOrg + inlined: true + inlined_as_list: true + migs_org_agriculture_data: + name: migs_org_agriculture_data + description: Data that complies with MigsOrg combined with Agriculture + title: MigsOrgAgriculture data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - administration - - animal - - antimicrobial - - food - - route - slot_uri: MIXS:0001246 - multivalued: false - range: string - required: false - recommended: false - animal_am_use: - name: animal_am_use - description: The prescribed intended use of or the condition treated by the antimicrobial - given to the food animal by any route of administration - title: food animal antimicrobial intended use - examples: - - value: shipping fever + domain: MixsCompliantData + slot_uri: MIXS:migs_org_agriculture_data + multivalued: true + range: MigsOrgAgriculture + inlined: true + inlined_as_list: true + migs_org_air_data: + name: migs_org_air_data + description: Data that complies with MigsOrg combined with Air + title: MigsOrgAir data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - animal - - antimicrobial - - food - - use - slot_uri: MIXS:0001247 - multivalued: false - range: string - required: false - recommended: false - animal_body_cond: - name: animal_body_cond - description: Body condition scoring is a production management tool used to evaluate - overall health and nutritional needs of a food animal. Because there are different - scoring systems, this field is restricted to three categories - title: food animal body condition - examples: - - value: under conditioned - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - animal - - body - - condition - - food - slot_uri: MIXS:0001248 - multivalued: false - range: ANIMAL_BODY_COND_ENUM - required: false - recommended: false - animal_diet: - name: animal_diet - annotations: - Expected_value: - tag: Expected_value - value: text or FOODON_03309997 - description: If the isolate is from a food animal, the type of diet eaten by the - food animal. Please list the main food staple and the setting, if appropriate. For - a list of acceptable animal feed terms or categories, please see http://www.feedipedia.org. Multiple - terms may apply and can be separated by pipes |Food product for animal covers - foods intended for consumption by domesticated animals. Consult http://purl.obolibrary.org/obo/FOODON_03309997. - If the proper descriptor is not listed please use text to describe the food - type. Multiple terms can be separated by one or more pipes. If the proper descriptor - is not listed please use text to describe the food product type - title: food animal source diet - examples: - - value: Hay [FOODON:03301763] - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - animal - - diet - - food - - source - string_serialization: '{text}' - slot_uri: MIXS:0001130 + domain: MixsCompliantData + slot_uri: MIXS:migs_org_air_data multivalued: true - required: false - recommended: false - animal_feed_equip: - name: animal_feed_equip - annotations: - Expected_value: - tag: Expected_value - value: EOL:0001757 - description: Description of the feeding equipment used for livestock. This field - accepts terms listed under feed delivery (http://opendata.inra.fr/EOL/EOL_0001757). - Multiple terms can be separated by pipes - title: animal feeding equipment - examples: - - value: self feeding [EOL:0001645]| straight feed trough [EOL:0001661] + range: MigsOrgAir + inlined: true + inlined_as_list: true + migs_org_built_environment_data: + name: migs_org_built_environment_data + description: Data that complies with MigsOrg combined with BuiltEnvironment + title: MigsOrgBuiltEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - animal - - equipment - string_serialization: '{termLabel} [{termID}]' - slot_uri: MIXS:0001113 + domain: MixsCompliantData + slot_uri: MIXS:migs_org_built_environment_data multivalued: true - required: false - recommended: false - animal_group_size: - name: animal_group_size - description: The number of food animals of the same species that are maintained - together as a unit, i.e. a herd or flock - title: food animal group size - examples: - - value: '80' + range: MigsOrgBuiltEnvironment + inlined: true + inlined_as_list: true + migs_org_food_animal_and_animal_feed_data: + name: migs_org_food_animal_and_animal_feed_data + description: Data that complies with MigsOrg combined with FoodAnimalAndAnimalFeed + title: MigsOrgFoodAnimalAndAnimalFeed data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - animal - - food - - size - slot_uri: MIXS:0001129 - multivalued: false - range: integer - required: false - recommended: false - animal_housing: - name: animal_housing - description: Description of the housing system of the livestock. This field accepts - terms listed under terrestrial management housing system (http://opendata.inra.fr/EOL/EOL_0001605) - title: animal housing system - examples: - - value: pen rearing system [EOL:0001636] + domain: MixsCompliantData + slot_uri: MIXS:migs_org_food_animal_and_animal_feed_data + multivalued: true + range: MigsOrgFoodAnimalAndAnimalFeed + inlined: true + inlined_as_list: true + migs_org_food_farm_environment_data: + name: migs_org_food_farm_environment_data + description: Data that complies with MigsOrg combined with FoodFarmEnvironment + title: MigsOrgFoodFarmEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - animal - slot_uri: MIXS:0001180 + domain: MixsCompliantData + slot_uri: MIXS:migs_org_food_farm_environment_data multivalued: true - range: string - required: false - recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ - structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ - interpolated: true - partial_match: true - animal_intrusion: - name: animal_intrusion - description: Identification of animals intruding on the sample or sample site - including invertebrates (such as pests or pollinators) and vertebrates (such - as wildlife or domesticated animals). This field accepts terms under organism - (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification - numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms - can be separated by pipes - title: animal intrusion near sample source - examples: - - value: Thripidae [NCBITaxon:45053] + range: MigsOrgFoodFarmEnvironment + inlined: true + inlined_as_list: true + migs_org_food_food_production_facility_data: + name: migs_org_food_food_production_facility_data + description: Data that complies with MigsOrg combined with FoodFoodProductionFacility + title: MigsOrgFoodFoodProductionFacility data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - animal - - sample - - source - slot_uri: MIXS:0001114 + domain: MixsCompliantData + slot_uri: MIXS:migs_org_food_food_production_facility_data multivalued: true - range: string - required: false - recommended: false - pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ - structured_pattern: - syntax: ^({termLabel} \[{termID}\])|{integer}$ - interpolated: true - partial_match: true - animal_sex: - name: animal_sex - description: The sex and reproductive status of the food animal - title: food animal source sex category - examples: - - value: castrated male + range: MigsOrgFoodFoodProductionFacility + inlined: true + inlined_as_list: true + migs_org_food_human_foods_data: + name: migs_org_food_human_foods_data + description: Data that complies with MigsOrg combined with FoodHumanFoods + title: MigsOrgFoodHumanFoods data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - animal - - food - - source - slot_uri: MIXS:0001249 - multivalued: false - range: ANIMAL_SEX_ENUM - required: false - recommended: false - annot: - name: annot - annotations: - Expected_value: - tag: Expected_value - value: name of tool or pipeline used, or annotation source description - description: Tool used for annotation, or for cases where annotation was provided - by a community jamboree or model organism database rather than by a specific - submitter - title: annotation - examples: - - value: prokka - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:migs_org_food_human_foods_data + multivalued: true + range: MigsOrgFoodHumanFoods + inlined: true + inlined_as_list: true + migs_org_host_associated_data: + name: migs_org_host_associated_data + description: Data that complies with MigsOrg combined with HostAssociated + title: MigsOrgHostAssociated data from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text}' - slot_uri: MIXS:0000059 - multivalued: false - annual_precpt: - name: annual_precpt - annotations: - Preferred_unit: - tag: Preferred_unit - value: millimeter - description: The average of all annual precipitation values known, or an estimated - equivalent value derived by such methods as regional indexes or Isohyetal maps - title: mean annual precipitation + domain: MixsCompliantData + slot_uri: MIXS:migs_org_host_associated_data + multivalued: true + range: MigsOrgHostAssociated + inlined: true + inlined_as_list: true + migs_org_human_associated_data: + name: migs_org_human_associated_data + description: Data that complies with MigsOrg combined with HumanAssociated + title: MigsOrgHumanAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - mean - slot_uri: MIXS:0000644 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - annual_temp: - name: annual_temp - annotations: - Preferred_unit: - tag: Preferred_unit - value: degree Celsius - description: Mean annual temperature - title: mean annual temperature - examples: - - value: 12.5 degree Celsius + domain: MixsCompliantData + slot_uri: MIXS:migs_org_human_associated_data + multivalued: true + range: MigsOrgHumanAssociated + inlined: true + inlined_as_list: true + migs_org_human_gut_data: + name: migs_org_human_gut_data + description: Data that complies with MigsOrg combined with HumanGut + title: MigsOrgHumanGut data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - mean - - temperature - slot_uri: MIXS:0000642 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - antibiotic_regm: - name: antibiotic_regm - annotations: - Expected_value: - tag: Expected_value - value: antibiotic name;antibiotic amount;treatment interval and duration - Preferred_unit: - tag: Preferred_unit - value: milligram - description: Information about treatment involving antibiotic administration; - should include the name of antibiotic, amount administered, treatment regimen - including how many times the treatment was repeated, how long each treatment - lasted, and the start and end time of the entire treatment; can include multiple - antibiotic regimens - title: antibiotic regimen - examples: - - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + domain: MixsCompliantData + slot_uri: MIXS:migs_org_human_gut_data + multivalued: true + range: MigsOrgHumanGut + inlined: true + inlined_as_list: true + migs_org_human_oral_data: + name: migs_org_human_oral_data + description: Data that complies with MigsOrg combined with HumanOral + title: MigsOrgHumanOral data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - regimen - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000553 + domain: MixsCompliantData + slot_uri: MIXS:migs_org_human_oral_data multivalued: true - required: false - recommended: false - api: - name: api - annotations: - Preferred_unit: - tag: Preferred_unit - value: degrees API - description: 'API gravity is a measure of how heavy or light a petroleum liquid - is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. - 31.1 API)' - title: API gravity - examples: - - value: 31.1 API + range: MigsOrgHumanOral + inlined: true + inlined_as_list: true + migs_org_human_skin_data: + name: migs_org_human_skin_data + description: Data that complies with MigsOrg combined with HumanSkin + title: MigsOrgHumanSkin data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000157 - multivalued: false - range: string - required: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - arch_struc: - name: arch_struc - description: An architectural structure is a human-made, free-standing, immobile - outdoor construction - title: architectural structure - examples: - - value: shed + domain: MixsCompliantData + slot_uri: MIXS:migs_org_human_skin_data + multivalued: true + range: MigsOrgHumanSkin + inlined: true + inlined_as_list: true + migs_org_human_vaginal_data: + name: migs_org_human_vaginal_data + description: Data that complies with MigsOrg combined with HumanVaginal + title: MigsOrgHumanVaginal data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000774 - multivalued: false - range: ARCH_STRUC_ENUM - required: false - recommended: false - area_samp_size: - name: area_samp_size - annotations: - Expected_value: - tag: Expected_value - value: measurement value - Preferred_unit: - tag: Preferred_unit - value: centimeter - description: The total amount or size (volume (ml), mass (g) or area (m2) ) of - sample collected - title: area sampled size - examples: - - value: 12 centimeter x 12 centimeter + domain: MixsCompliantData + slot_uri: MIXS:migs_org_human_vaginal_data + multivalued: true + range: MigsOrgHumanVaginal + inlined: true + inlined_as_list: true + migs_org_hydrocarbon_resources_cores_data: + name: migs_org_hydrocarbon_resources_cores_data + description: Data that complies with MigsOrg combined with HydrocarbonResourcesCores + title: MigsOrgHydrocarbonResourcesCores data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - area - - sample - - size - string_serialization: '{integer} {unit} x {integer} {unit}' - slot_uri: MIXS:0001255 - multivalued: false - required: false - recommended: false - aromatics_pc: - name: aromatics_pc - annotations: - Preferred_unit: - tag: Preferred_unit - value: percent - description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis - method that divides crude oil components according to their polarizability - and polarity. There are three main methods to obtain SARA results. The most - popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: - https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' - title: aromatics wt% + domain: MixsCompliantData + slot_uri: MIXS:migs_org_hydrocarbon_resources_cores_data + multivalued: true + range: MigsOrgHydrocarbonResourcesCores + inlined: true + inlined_as_list: true + migs_org_hydrocarbon_resources_fluids_swabs_data: + name: migs_org_hydrocarbon_resources_fluids_swabs_data + description: Data that complies with MigsOrg combined with HydrocarbonResourcesFluidsSwabs + title: MigsOrgHydrocarbonResourcesFluidsSwabs data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000133 - multivalued: false - range: string - recommended: true - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{name};{float} {unit}$ - interpolated: true - partial_match: true - asphaltenes_pc: - name: asphaltenes_pc - annotations: - Preferred_unit: - tag: Preferred_unit - value: percent - description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis - method that divides crude oil components according to their polarizability - and polarity. There are three main methods to obtain SARA results. The most - popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: - https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' - title: asphaltenes wt% + domain: MixsCompliantData + slot_uri: MIXS:migs_org_hydrocarbon_resources_fluids_swabs_data + multivalued: true + range: MigsOrgHydrocarbonResourcesFluidsSwabs + inlined: true + inlined_as_list: true + migs_org_microbial_mat_biofilm_data: + name: migs_org_microbial_mat_biofilm_data + description: Data that complies with MigsOrg combined with MicrobialMatBiofilm + title: MigsOrgMicrobialMatBiofilm data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000135 - multivalued: false - range: string - recommended: true - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{name};{float} {unit}$ - interpolated: true - partial_match: true - assembly_name: - name: assembly_name - annotations: - Expected_value: - tag: Expected_value - value: name and version of assembly - description: Name/version of the assembly provided by the submitter that is used - in the genome browsers and in the community - title: assembly name - examples: - - value: HuRef, JCVI_ISG_i3_1.0 - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:migs_org_microbial_mat_biofilm_data + multivalued: true + range: MigsOrgMicrobialMatBiofilm + inlined: true + inlined_as_list: true + migs_org_miscellaneous_natural_or_artificial_environment_data: + name: migs_org_miscellaneous_natural_or_artificial_environment_data + description: Data that complies with MigsOrg combined with MiscellaneousNaturalOrArtificialEnvironment + title: MigsOrgMiscellaneousNaturalOrArtificialEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text} {text}' - slot_uri: MIXS:0000057 - multivalued: false - assembly_qual: - name: assembly_qual - annotations: - Expected_value: - tag: Expected_value - value: enumeration - description: 'The assembly quality category is based on sets of criteria outlined - for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, - contiguous sequence per replicon without gaps or ambiguities with a consensus - error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments - where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes - and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no - review of assembly other than reporting of standard assembly statistics. Low - Quality Draft:Many fragments with little to no review of assembly other than - reporting of standard assembly statistics. Assembly statistics include, but - are not limited to total assembly size, number of contigs, contig N50/L50, and - maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence - per replicon without gaps or ambiguities, with extensive manual review and editing - to annotate putative gene functions and transcriptional units. High-quality - draft genome: One or multiple fragments, totaling 90% of the expected genome - or replicon sequence or predicted complete. Genome fragment(s): One or multiple - fragments, totalling < 90% of the expected genome or replicon sequence, or for - which no genome size could be estimated' - title: assembly quality - examples: - - value: High-quality draft genome - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:migs_org_miscellaneous_natural_or_artificial_environment_data + multivalued: true + range: MigsOrgMiscellaneousNaturalOrArtificialEnvironment + inlined: true + inlined_as_list: true + migs_org_plant_associated_data: + name: migs_org_plant_associated_data + description: Data that complies with MigsOrg combined with PlantAssociated + title: MigsOrgPlantAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - quality - string_serialization: '[Finished genome|High-quality draft genome|Medium-quality - draft genome|Low-quality draft genome|Genome fragment(s)]' - slot_uri: MIXS:0000056 - multivalued: false - assembly_software: - name: assembly_software - description: Tool(s) used for assembly, including version number and parameters - title: assembly software - examples: - - value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:migs_org_plant_associated_data + multivalued: true + range: MigsOrgPlantAssociated + inlined: true + inlined_as_list: true + migs_org_sediment_data: + name: migs_org_sediment_data + description: Data that complies with MigsOrg combined with Sediment + title: MigsOrgSediment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - software - slot_uri: MIXS:0000058 - multivalued: false - range: string - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{software};{version};{parameters}$ - interpolated: true - partial_match: true - associated_resource: - name: associated_resource - annotations: - Expected_value: - tag: Expected_value - value: reference to resource - description: A related resource that is referenced, cited, or otherwise associated - to the sequence - title: relevant electronic resources - examples: - - value: http://www.earthmicrobiome.org/ - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:migs_org_sediment_data + multivalued: true + range: MigsOrgSediment + inlined: true + inlined_as_list: true + migs_org_soil_data: + name: migs_org_soil_data + description: Data that complies with MigsOrg combined with Soil + title: MigsOrgSoil data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - resource - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000091 + domain: MixsCompliantData + slot_uri: MIXS:migs_org_soil_data multivalued: true - recommended: true - association_duration: - name: association_duration - annotations: - Preferred_unit: - tag: Preferred_unit - value: year, day, hour - description: Time spent in host of the symbiotic organism at the time of sampling; - relevant scale depends on symbiotic organism and study - title: duration of association with the host + range: MigsOrgSoil + inlined: true + inlined_as_list: true + migs_org_symbiont_associated_data: + name: migs_org_symbiont_associated_data + description: Data that complies with MigsOrg combined with SymbiontAssociated + title: MigsOrgSymbiontAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - duration - - host - - host. - - period - slot_uri: MIXS:0001299 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - atmospheric_data: - name: atmospheric_data - annotations: - Expected_value: - tag: Expected_value - value: atmospheric data name;measurement value - description: Measurement of atmospheric data; can include multiple data - title: atmospheric data - examples: - - value: wind speed;9 knots + domain: MixsCompliantData + slot_uri: MIXS:migs_org_symbiont_associated_data + multivalued: true + range: MigsOrgSymbiontAssociated + inlined: true + inlined_as_list: true + migs_org_wastewater_sludge_data: + name: migs_org_wastewater_sludge_data + description: Data that complies with MigsOrg combined with WastewaterSludge + title: MigsOrgWastewaterSludge data from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0001097 + domain: MixsCompliantData + slot_uri: MIXS:migs_org_wastewater_sludge_data multivalued: true - required: false - recommended: false - avg_dew_point: - name: avg_dew_point - annotations: - Preferred_unit: - tag: Preferred_unit - value: degree Celsius - description: The average of dew point measures taken at the beginning of every - hour over a 24 hour period on the sampling day - title: average dew point - examples: - - value: 25.5 degree Celsius + range: MigsOrgWastewaterSludge + inlined: true + inlined_as_list: true + migs_org_water_data: + name: migs_org_water_data + description: Data that complies with MigsOrg combined with Water + title: MigsOrgWater data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - average - slot_uri: MIXS:0000141 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - avg_occup: - name: avg_occup - description: Daily average occupancy of room. Indicate the number of person(s) - daily occupying the sampling room - title: average daily occupancy + domain: MixsCompliantData + slot_uri: MIXS:migs_org_water_data + multivalued: true + range: MigsOrgWater + inlined: true + inlined_as_list: true + migs_pl_data: + name: migs_pl_data + description: Data that complies with checklist MigsPl + title: MigsPl data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - average - slot_uri: MIXS:0000775 - multivalued: false - range: float - required: false - recommended: false - avg_temp: - name: avg_temp - annotations: - Preferred_unit: - tag: Preferred_unit - value: degree Celsius - description: The average of temperatures taken at the beginning of every hour - over a 24 hour period on the sampling day - title: average temperature - examples: - - value: 12.5 degree Celsius + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_data + multivalued: true + range: MigsPl + inlined: true + inlined_as_list: true + migs_pl_agriculture_data: + name: migs_pl_agriculture_data + description: Data that complies with MigsPl combined with Agriculture + title: MigsPlAgriculture data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - average - - temperature - slot_uri: MIXS:0000142 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - bac_prod: - name: bac_prod - annotations: - Preferred_unit: - tag: Preferred_unit - value: milligram per cubic meter per day - description: Bacterial production in the water column measured by isotope uptake - title: bacterial production - examples: - - value: 5 milligram per cubic meter per day + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_agriculture_data + multivalued: true + range: MigsPlAgriculture + inlined: true + inlined_as_list: true + migs_pl_air_data: + name: migs_pl_air_data + description: Data that complies with MigsPl combined with Air + title: MigsPlAir data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - production - slot_uri: MIXS:0000683 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - bac_resp: - name: bac_resp - annotations: - Preferred_unit: - tag: Preferred_unit - value: milligram per cubic meter per day, micromole oxygen per liter per hour - description: Measurement of bacterial respiration in the water column - title: bacterial respiration - examples: - - value: 300 micromole oxygen per liter per hour + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_air_data + multivalued: true + range: MigsPlAir + inlined: true + inlined_as_list: true + migs_pl_built_environment_data: + name: migs_pl_built_environment_data + description: Data that complies with MigsPl combined with BuiltEnvironment + title: MigsPlBuiltEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000684 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - bacteria_carb_prod: - name: bacteria_carb_prod - description: Measurement of bacterial carbon production - title: bacterial carbon production - examples: - - value: 2.53 microgram per liter per hour + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_built_environment_data + multivalued: true + range: MigsPlBuiltEnvironment + inlined: true + inlined_as_list: true + migs_pl_food_animal_and_animal_feed_data: + name: migs_pl_food_animal_and_animal_feed_data + description: Data that complies with MigsPl combined with FoodAnimalAndAnimalFeed + title: MigsPlFoodAnimalAndAnimalFeed data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - carbon - - production - slot_uri: MIXS:0000173 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - bacterial_density: - name: bacterial_density - annotations: - Preferred_unit: - tag: Preferred_unit - value: colony forming units per milliliter; colony forming units per gram - of dry weight - description: Number of bacteria in sample, as defined by bacteria density (http://purl.obolibrary.org/obo/GENEPIO_0000043) - title: bacteria density - examples: - - value: 10 colony forming units per gram dry weight + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_food_animal_and_animal_feed_data + multivalued: true + range: MigsPlFoodAnimalAndAnimalFeed + inlined: true + inlined_as_list: true + migs_pl_food_farm_environment_data: + name: migs_pl_food_farm_environment_data + description: Data that complies with MigsPl combined with FoodFarmEnvironment + title: MigsPlFoodFarmEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - density - slot_uri: MIXS:0001194 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - barometric_press: - name: barometric_press - annotations: - Preferred_unit: - tag: Preferred_unit - value: millibar - description: Force per unit area exerted against a surface by the weight of air - above that surface - title: barometric pressure - examples: - - value: 5 millibar + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_food_farm_environment_data + multivalued: true + range: MigsPlFoodFarmEnvironment + inlined: true + inlined_as_list: true + migs_pl_food_food_production_facility_data: + name: migs_pl_food_food_production_facility_data + description: Data that complies with MigsPl combined with FoodFoodProductionFacility + title: MigsPlFoodFoodProductionFacility data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - pressure - slot_uri: MIXS:0000096 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - basin: - name: basin - description: Name of the basin (e.g. Campos) - title: basin name - examples: - - value: Campos + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_food_food_production_facility_data + multivalued: true + range: MigsPlFoodFoodProductionFacility + inlined: true + inlined_as_list: true + migs_pl_food_human_foods_data: + name: migs_pl_food_human_foods_data + description: Data that complies with MigsPl combined with FoodHumanFoods + title: MigsPlFoodHumanFoods data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000290 - multivalued: false - range: string - required: true - bathroom_count: - name: bathroom_count - description: The number of bathrooms in the building - title: bathroom count - examples: - - value: '1' + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_food_human_foods_data + multivalued: true + range: MigsPlFoodHumanFoods + inlined: true + inlined_as_list: true + migs_pl_host_associated_data: + name: migs_pl_host_associated_data + description: Data that complies with MigsPl combined with HostAssociated + title: MigsPlHostAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - count - slot_uri: MIXS:0000776 - multivalued: false - range: integer - required: false - recommended: false - bedroom_count: - name: bedroom_count - description: The number of bedrooms in the building - title: bedroom count - examples: - - value: '2' + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_host_associated_data + multivalued: true + range: MigsPlHostAssociated + inlined: true + inlined_as_list: true + migs_pl_human_associated_data: + name: migs_pl_human_associated_data + description: Data that complies with MigsPl combined with HumanAssociated + title: MigsPlHumanAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - count - slot_uri: MIXS:0000777 - multivalued: false - range: integer - required: false - recommended: false - benzene: - name: benzene - annotations: - Preferred_unit: - tag: Preferred_unit - value: milligram per liter, parts per million - description: Concentration of benzene in the sample - title: benzene - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000153 - multivalued: false - range: string - recommended: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - bin_param: - name: bin_param - description: The parameters that have been applied during the extraction of genomes - from metagenomic datasets - title: binning parameters - examples: - - value: coverage - description: was 'coverage and kmer' - - value: kmer - description: was coverage and kmer - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_human_associated_data + multivalued: true + range: MigsPlHumanAssociated + inlined: true + inlined_as_list: true + migs_pl_human_gut_data: + name: migs_pl_human_gut_data + description: Data that complies with MigsPl combined with HumanGut + title: MigsPlHumanGut data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - parameter - slot_uri: MIXS:0000077 - range: BIN_PARAM_ENUM - bin_software: - name: bin_software - annotations: - Expected_value: - tag: Expected_value - value: names and versions of software(s) used - description: Tool(s) used for the extraction of genomes from metagenomic datasets, - where possible include a product ID (PID) of the tool(s) used - title: binning software - examples: - - value: MetaCluster-TA (RRID:SCR_004599), MaxBin (biotools:maxbin) - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_human_gut_data + multivalued: true + range: MigsPlHumanGut + inlined: true + inlined_as_list: true + migs_pl_human_oral_data: + name: migs_pl_human_oral_data + description: Data that complies with MigsPl combined with HumanOral + title: MigsPlHumanOral data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - software - string_serialization: '{software};{version}{PID}' - slot_uri: MIXS:0000078 - multivalued: false - biochem_oxygen_dem: - name: biochem_oxygen_dem - annotations: - Preferred_unit: - tag: Preferred_unit - value: milligram per liter - description: Amount of dissolved oxygen needed by aerobic biological organisms - in a body of water to break down organic material present in a given water sample - at certain temperature over a specific time period - title: biochemical oxygen demand + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_human_oral_data + multivalued: true + range: MigsPlHumanOral + inlined: true + inlined_as_list: true + migs_pl_human_skin_data: + name: migs_pl_human_skin_data + description: Data that complies with MigsPl combined with HumanSkin + title: MigsPlHumanSkin data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - oxygen - slot_uri: MIXS:0000653 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - biocide: - name: biocide - annotations: - Expected_value: - tag: Expected_value - value: name;name;timestamp - description: List of biocides (commercial name of product and supplier) and date - of administration - title: biocide administration - examples: - - value: ALPHA 1427;Baker Hughes;2008-01-23 + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_human_skin_data + multivalued: true + range: MigsPlHumanSkin + inlined: true + inlined_as_list: true + migs_pl_human_vaginal_data: + name: migs_pl_human_vaginal_data + description: Data that complies with MigsPl combined with HumanVaginal + title: MigsPlHumanVaginal data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - administration - string_serialization: '{text};{text};{timestamp}' - slot_uri: MIXS:0001011 - multivalued: false - recommended: true - biocide_admin_method: - name: biocide_admin_method - annotations: - Expected_value: - tag: Expected_value - value: measurement value;frequency;duration;duration - Preferred_unit: - tag: Preferred_unit - value: milligram per liter - description: Method of biocide administration (dose, frequency, duration, time - elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 - days) - title: biocide administration method + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_human_vaginal_data + multivalued: true + range: MigsPlHumanVaginal + inlined: true + inlined_as_list: true + migs_pl_hydrocarbon_resources_cores_data: + name: migs_pl_hydrocarbon_resources_cores_data + description: Data that complies with MigsPl combined with HydrocarbonResourcesCores + title: MigsPlHydrocarbonResourcesCores data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - administration - - method - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}' - slot_uri: MIXS:0000456 - multivalued: false - recommended: true - biocide_used: - name: biocide_used - annotations: - Expected_value: - tag: Expected_value - value: commercial name of biocide, active ingredient in biocide or class of - biocide - description: Substance intended for preventing, neutralizing, destroying, repelling, - or mitigating the effects of any pest or microorganism; that inhibits the growth, - reproduction, and activity of organisms, including fungal cells; decreases the - number of fungi or pests present; deters microbial growth and degradation of - other ingredients in the formulation. Indicate the biocide used on the location - where the sample was taken. Multiple terms can be separated by pipes - title: biocide - examples: - - value: Quaternary ammonium compound|SterBac + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_hydrocarbon_resources_cores_data + multivalued: true + range: MigsPlHydrocarbonResourcesCores + inlined: true + inlined_as_list: true + migs_pl_hydrocarbon_resources_fluids_swabs_data: + name: migs_pl_hydrocarbon_resources_fluids_swabs_data + description: Data that complies with MigsPl combined with HydrocarbonResourcesFluidsSwabs + title: MigsPlHydrocarbonResourcesFluidsSwabs data from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text}' - slot_uri: MIXS:0001258 + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_hydrocarbon_resources_fluids_swabs_data multivalued: true - required: false - recommended: false - biol_stat: - name: biol_stat - annotations: - Expected_value: - tag: Expected_value - value: enumeration - description: The level of genome modification - title: biological status - examples: - - value: natural + range: MigsPlHydrocarbonResourcesFluidsSwabs + inlined: true + inlined_as_list: true + migs_pl_microbial_mat_biofilm_data: + name: migs_pl_microbial_mat_biofilm_data + description: Data that complies with MigsPl combined with MicrobialMatBiofilm + title: MigsPlMicrobialMatBiofilm data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - status - string_serialization: '[wild|natural|semi-natural|inbred line|breeder''s line|hybrid|clonal - selection|mutant]' - slot_uri: MIXS:0000858 - multivalued: false - required: false - recommended: false - biomass: - name: biomass - annotations: - Expected_value: - tag: Expected_value - value: biomass type;measurement value - Preferred_unit: - tag: Preferred_unit - value: ton, kilogram, gram - description: Amount of biomass; should include the name for the part of biomass - measured, e.g. Microbial, total. Can include multiple measurements - title: biomass - examples: - - value: total;20 gram + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_microbial_mat_biofilm_data + multivalued: true + range: MigsPlMicrobialMatBiofilm + inlined: true + inlined_as_list: true + migs_pl_miscellaneous_natural_or_artificial_environment_data: + name: migs_pl_miscellaneous_natural_or_artificial_environment_data + description: Data that complies with MigsPl combined with MiscellaneousNaturalOrArtificialEnvironment + title: MigsPlMiscellaneousNaturalOrArtificialEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - biomass - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000174 + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_miscellaneous_natural_or_artificial_environment_data multivalued: true - required: false - recommended: false - biotic_regm: - name: biotic_regm - description: Information about treatment(s) involving use of biotic factors, such - as bacteria, viruses or fungi - title: biotic regimen - examples: - - value: sample inoculated with Rhizobium spp. Culture + range: MigsPlMiscellaneousNaturalOrArtificialEnvironment + inlined: true + inlined_as_list: true + migs_pl_plant_associated_data: + name: migs_pl_plant_associated_data + description: Data that complies with MigsPl combined with PlantAssociated + title: MigsPlPlantAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - regimen - slot_uri: MIXS:0001038 + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_plant_associated_data multivalued: true - range: string - biotic_relationship: - name: biotic_relationship - description: Description of relationship(s) between the subject organism and other - organism(s) it is associated with. E.g., parasite on species X; mutualist with - species Y. The target organism is the subject of the relationship, and the other - organism(s) is the object - title: observed biotic relationship - examples: - - value: free living - in_subset: - - nucleic acid sequence source + range: MigsPlPlantAssociated + inlined: true + inlined_as_list: true + migs_pl_sediment_data: + name: migs_pl_sediment_data + description: Data that complies with MigsPl combined with Sediment + title: MigsPlSediment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - observed - - relationship - slot_uri: MIXS:0000028 - multivalued: false - range: BIOTIC_RELATIONSHIP_ENUM - birth_control: - name: birth_control - annotations: - Expected_value: - tag: Expected_value - value: medication name - description: Specification of birth control medication used - title: birth control + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_sediment_data + multivalued: true + range: MigsPlSediment + inlined: true + inlined_as_list: true + migs_pl_soil_data: + name: migs_pl_soil_data + description: Data that complies with MigsPl combined with Soil + title: MigsPlSoil data from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text}' - slot_uri: MIXS:0000286 - multivalued: false - required: false - recommended: false - bishomohopanol: - name: bishomohopanol - annotations: - Preferred_unit: - tag: Preferred_unit - value: microgram per liter, microgram per gram - description: Concentration of bishomohopanol - title: bishomohopanol - examples: - - value: 14 microgram per liter + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_soil_data + multivalued: true + range: MigsPlSoil + inlined: true + inlined_as_list: true + migs_pl_symbiont_associated_data: + name: migs_pl_symbiont_associated_data + description: Data that complies with MigsPl combined with SymbiontAssociated + title: MigsPlSymbiontAssociated data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000175 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - blood_blood_disord: - name: blood_blood_disord - description: History of blood disorders; can include multiple disorders. The - terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - hematopoietic system disease (https://disease-ontology.org/?id=DOID:74) - title: blood/blood disorder + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_symbiont_associated_data + multivalued: true + range: MigsPlSymbiontAssociated + inlined: true + inlined_as_list: true + migs_pl_wastewater_sludge_data: + name: migs_pl_wastewater_sludge_data + description: Data that complies with MigsPl combined with WastewaterSludge + title: MigsPlWastewaterSludge data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - disorder - slot_uri: MIXS:0000271 + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_wastewater_sludge_data multivalued: true - range: string - required: false - recommended: false - blood_press_diast: - name: blood_press_diast - annotations: - Preferred_unit: - tag: Preferred_unit - value: millimeter mercury - description: Resting diastolic blood pressure, measured as mm mercury - title: host blood pressure diastolic + range: MigsPlWastewaterSludge + inlined: true + inlined_as_list: true + migs_pl_water_data: + name: migs_pl_water_data + description: Data that complies with MigsPl combined with Water + title: MigsPlWater data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - pressure - slot_uri: MIXS:0000258 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - blood_press_syst: - name: blood_press_syst - annotations: - Preferred_unit: - tag: Preferred_unit - value: millimeter mercury - description: Resting systolic blood pressure, measured as mm mercury - title: host blood pressure systolic + domain: MixsCompliantData + slot_uri: MIXS:migs_pl_water_data + multivalued: true + range: MigsPlWater + inlined: true + inlined_as_list: true + migs_vi_data: + name: migs_vi_data + description: Data that complies with checklist MigsVi + title: MigsVi data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - pressure - slot_uri: MIXS:0000259 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - bromide: - name: bromide - annotations: - Preferred_unit: - tag: Preferred_unit - value: parts per million - description: Concentration of bromide - title: bromide - examples: - - value: 0.05 parts per million + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_data + multivalued: true + range: MigsVi + inlined: true + inlined_as_list: true + migs_vi_agriculture_data: + name: migs_vi_agriculture_data + description: Data that complies with MigsVi combined with Agriculture + title: MigsViAgriculture data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000176 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - build_docs: - name: build_docs - description: The building design, construction and operation documents - title: design, construction, and operation documents - examples: - - value: maintenance plans + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_agriculture_data + multivalued: true + range: MigsViAgriculture + inlined: true + inlined_as_list: true + migs_vi_air_data: + name: migs_vi_air_data + description: Data that complies with MigsVi combined with Air + title: MigsViAir data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - documents - slot_uri: MIXS:0000787 - multivalued: false - range: BUILD_DOCS_ENUM - required: false - recommended: false - build_occup_type: - name: build_occup_type - description: The primary function for which a building or discrete part of a building - is intended to be used - title: building occupancy type - examples: - - value: market + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_air_data + multivalued: true + range: MigsViAir + inlined: true + inlined_as_list: true + migs_vi_built_environment_data: + name: migs_vi_built_environment_data + description: Data that complies with MigsVi combined with BuiltEnvironment + title: MigsViBuiltEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - type - slot_uri: MIXS:0000761 + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_built_environment_data multivalued: true - range: BUILD_OCCUP_TYPE_ENUM - required: true - building_setting: - name: building_setting - description: A location (geography) where a building is set - title: building setting - examples: - - value: rural + range: MigsViBuiltEnvironment + inlined: true + inlined_as_list: true + migs_vi_food_animal_and_animal_feed_data: + name: migs_vi_food_animal_and_animal_feed_data + description: Data that complies with MigsVi combined with FoodAnimalAndAnimalFeed + title: MigsViFoodAnimalAndAnimalFeed data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000768 - multivalued: false - range: BUILDING_SETTING_ENUM - required: true - built_struc_age: - name: built_struc_age - annotations: - Preferred_unit: - tag: Preferred_unit - value: year - description: The age of the built structure since construction - title: built structure age - examples: - - value: 15 years + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_food_animal_and_animal_feed_data + multivalued: true + range: MigsViFoodAnimalAndAnimalFeed + inlined: true + inlined_as_list: true + migs_vi_food_farm_environment_data: + name: migs_vi_food_farm_environment_data + description: Data that complies with MigsVi combined with FoodFarmEnvironment + title: MigsViFoodFarmEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - age - slot_uri: MIXS:0000145 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - built_struc_set: - name: built_struc_set - description: The characterization of the location of the built structure as high - or low human density - title: built structure setting - examples: - - value: rural + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_food_farm_environment_data + multivalued: true + range: MigsViFoodFarmEnvironment + inlined: true + inlined_as_list: true + migs_vi_food_food_production_facility_data: + name: migs_vi_food_food_production_facility_data + description: Data that complies with MigsVi combined with FoodFoodProductionFacility + title: MigsViFoodFoodProductionFacility data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000778 - multivalued: false - range: BUILT_STRUC_SET_ENUM - required: false - recommended: false - built_struc_type: - name: built_struc_type - description: A physical structure that is a body or assemblage of bodies in space - to form a system capable of supporting loads - title: built structure type + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_food_food_production_facility_data + multivalued: true + range: MigsViFoodFoodProductionFacility + inlined: true + inlined_as_list: true + migs_vi_food_human_foods_data: + name: migs_vi_food_human_foods_data + description: Data that complies with MigsVi combined with FoodHumanFoods + title: MigsViFoodHumanFoods data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - type - slot_uri: MIXS:0000721 - multivalued: false - range: string - required: false - recommended: false - calcium: - name: calcium - annotations: - Preferred_unit: - tag: Preferred_unit - value: milligram per liter, micromole per liter, parts per million - description: Concentration of calcium in the sample - title: calcium - examples: - - value: 0.2 micromole per liter + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_food_human_foods_data + multivalued: true + range: MigsViFoodHumanFoods + inlined: true + inlined_as_list: true + migs_vi_host_associated_data: + name: migs_vi_host_associated_data + description: Data that complies with MigsVi combined with HostAssociated + title: MigsViHostAssociated data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000432 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - carb_dioxide: - name: carb_dioxide - annotations: - Preferred_unit: - tag: Preferred_unit - value: micromole per liter, parts per million - description: Carbon dioxide (gas) amount or concentration at the time of sampling - title: carbon dioxide - examples: - - value: 410 parts per million - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - carbon - slot_uri: MIXS:0000097 - multivalued: false - range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - carb_monoxide: - name: carb_monoxide - annotations: - Preferred_unit: - tag: Preferred_unit - value: micromole per liter, parts per million - description: Carbon monoxide (gas) amount or concentration at the time of sampling - title: carbon monoxide - examples: - - value: 0.1 parts per million + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_host_associated_data + multivalued: true + range: MigsViHostAssociated + inlined: true + inlined_as_list: true + migs_vi_human_associated_data: + name: migs_vi_human_associated_data + description: Data that complies with MigsVi combined with HumanAssociated + title: MigsViHumanAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - carbon - slot_uri: MIXS:0000098 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - carb_nitro_ratio: - name: carb_nitro_ratio - annotations: - Expected_value: - tag: Expected_value - value: measurement value - description: Ratio of amount or concentrations of carbon to nitrogen - title: carbon/nitrogen ratio - examples: - - value: '0.417361111' + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_human_associated_data + multivalued: true + range: MigsViHumanAssociated + inlined: true + inlined_as_list: true + migs_vi_human_gut_data: + name: migs_vi_human_gut_data + description: Data that complies with MigsVi combined with HumanGut + title: MigsViHumanGut data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - carbon - - nitrogen - - ratio - string_serialization: '{float}:{float}' - slot_uri: MIXS:0000310 - range: float - required: false - recommended: false - ceil_area: - name: ceil_area - annotations: - Preferred_unit: - tag: Preferred_unit - value: square meter - description: The area of the ceiling space within the room - title: ceiling area - examples: - - value: 25 square meter + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_human_gut_data + multivalued: true + range: MigsViHumanGut + inlined: true + inlined_as_list: true + migs_vi_human_oral_data: + name: migs_vi_human_oral_data + description: Data that complies with MigsVi combined with HumanOral + title: MigsViHumanOral data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - area - - ceiling - slot_uri: MIXS:0000148 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - ceil_cond: - name: ceil_cond - description: The physical condition of the ceiling at the time of sampling; photos - or video preferred; use drawings to indicate location of damaged areas - title: ceiling condition - examples: - - value: damaged + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_human_oral_data + multivalued: true + range: MigsViHumanOral + inlined: true + inlined_as_list: true + migs_vi_human_skin_data: + name: migs_vi_human_skin_data + description: Data that complies with MigsVi combined with HumanSkin + title: MigsViHumanSkin data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - ceiling - - condition - slot_uri: MIXS:0000779 - multivalued: false - range: SHARED_ENUM_3 - required: false - recommended: false - ceil_finish_mat: - name: ceil_finish_mat - description: The type of material used to finish a ceiling - title: ceiling finish material - examples: - - value: stucco + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_human_skin_data + multivalued: true + range: MigsViHumanSkin + inlined: true + inlined_as_list: true + migs_vi_human_vaginal_data: + name: migs_vi_human_vaginal_data + description: Data that complies with MigsVi combined with HumanVaginal + title: MigsViHumanVaginal data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - ceiling - - material - slot_uri: MIXS:0000780 - multivalued: false - range: CEIL_FINISH_MAT_ENUM - required: false - recommended: false - ceil_struc: - name: ceil_struc - description: The construction format of the ceiling - title: ceiling structure - examples: - - value: concrete + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_human_vaginal_data + multivalued: true + range: MigsViHumanVaginal + inlined: true + inlined_as_list: true + migs_vi_hydrocarbon_resources_cores_data: + name: migs_vi_hydrocarbon_resources_cores_data + description: Data that complies with MigsVi combined with HydrocarbonResourcesCores + title: MigsViHydrocarbonResourcesCores data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - ceiling - slot_uri: MIXS:0000782 - multivalued: false - range: CEIL_STRUC_ENUM - required: false - recommended: false - ceil_texture: - name: ceil_texture - description: The feel, appearance, or consistency of a ceiling surface - title: ceiling texture - examples: - - value: popcorn + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_hydrocarbon_resources_cores_data + multivalued: true + range: MigsViHydrocarbonResourcesCores + inlined: true + inlined_as_list: true + migs_vi_hydrocarbon_resources_fluids_swabs_data: + name: migs_vi_hydrocarbon_resources_fluids_swabs_data + description: Data that complies with MigsVi combined with HydrocarbonResourcesFluidsSwabs + title: MigsViHydrocarbonResourcesFluidsSwabs data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - ceiling - - texture - slot_uri: MIXS:0000783 - multivalued: false - range: SHARED_ENUM_4 - required: false - recommended: false - ceil_thermal_mass: - name: ceil_thermal_mass - annotations: - Preferred_unit: - tag: Preferred_unit - value: joule per degree Celsius - description: The ability of the ceiling to provide inertia against temperature - fluctuations. Generally this means concrete that is exposed. A metal deck that - supports a concrete slab will act thermally as long as it is exposed to room - air flow - title: ceiling thermal mass + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_hydrocarbon_resources_fluids_swabs_data + multivalued: true + range: MigsViHydrocarbonResourcesFluidsSwabs + inlined: true + inlined_as_list: true + migs_vi_microbial_mat_biofilm_data: + name: migs_vi_microbial_mat_biofilm_data + description: Data that complies with MigsVi combined with MicrobialMatBiofilm + title: MigsViMicrobialMatBiofilm data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - ceiling - - mass - slot_uri: MIXS:0000143 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - ceil_type: - name: ceil_type - description: The type of ceiling according to the ceiling's appearance or construction - title: ceiling type - examples: - - value: coffered + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_microbial_mat_biofilm_data + multivalued: true + range: MigsViMicrobialMatBiofilm + inlined: true + inlined_as_list: true + migs_vi_miscellaneous_natural_or_artificial_environment_data: + name: migs_vi_miscellaneous_natural_or_artificial_environment_data + description: Data that complies with MigsVi combined with MiscellaneousNaturalOrArtificialEnvironment + title: MigsViMiscellaneousNaturalOrArtificialEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - ceiling - - type - slot_uri: MIXS:0000784 - multivalued: false - range: CEIL_TYPE_ENUM - required: false - recommended: false - ceil_water_mold: - name: ceil_water_mold - description: Signs of the presence of mold or mildew on the ceiling - title: ceiling signs of water/mold - examples: - - value: presence of mold visible + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_miscellaneous_natural_or_artificial_environment_data + multivalued: true + range: MigsViMiscellaneousNaturalOrArtificialEnvironment + inlined: true + inlined_as_list: true + migs_vi_plant_associated_data: + name: migs_vi_plant_associated_data + description: Data that complies with MigsVi combined with PlantAssociated + title: MigsViPlantAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - ceiling - slot_uri: MIXS:0000781 - multivalued: false - range: SHARED_ENUM_1 - required: false - recommended: false - chem_administration: - name: chem_administration - annotations: - Expected_value: - tag: Expected_value - value: CHEBI;timestamp - description: List of chemical compounds administered to the host or site where - sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can - include multiple compounds. For chemical entities of biological interest ontology - (chebi) (v 163), http://purl.bioontology.org/ontology/chebi - title: chemical administration - examples: - - value: agar [CHEBI:2509];2018-05-11T20:00Z + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_plant_associated_data + multivalued: true + range: MigsViPlantAssociated + inlined: true + inlined_as_list: true + migs_vi_sediment_data: + name: migs_vi_sediment_data + description: Data that complies with MigsVi combined with Sediment + title: MigsViSediment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - administration - string_serialization: '{termLabel} [{termID}];{timestamp}' - slot_uri: MIXS:0000751 + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_sediment_data multivalued: true - chem_mutagen: - name: chem_mutagen - annotations: - Expected_value: - tag: Expected_value - value: mutagen name;mutagen amount;treatment interval and duration - Preferred_unit: - tag: Preferred_unit - value: milligram per liter - description: Treatment involving use of mutagens; should include the name of mutagen, - amount administered, treatment regimen including how many times the treatment - was repeated, how long each treatment lasted, and the start and end time of - the entire treatment; can include multiple mutagen regimens - title: chemical mutagen - examples: - - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + range: MigsViSediment + inlined: true + inlined_as_list: true + migs_vi_soil_data: + name: migs_vi_soil_data + description: Data that complies with MigsVi combined with Soil + title: MigsViSoil data from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000555 + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_soil_data multivalued: true - required: false - recommended: false - chem_oxygen_dem: - name: chem_oxygen_dem - annotations: - Preferred_unit: - tag: Preferred_unit - value: milligram per liter - description: A measure of the capacity of water to consume oxygen during the decomposition - of organic matter and the oxidation of inorganic chemicals such as ammonia and - nitrite - title: chemical oxygen demand + range: MigsViSoil + inlined: true + inlined_as_list: true + migs_vi_symbiont_associated_data: + name: migs_vi_symbiont_associated_data + description: Data that complies with MigsVi combined with SymbiontAssociated + title: MigsViSymbiontAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - oxygen - slot_uri: MIXS:0000656 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - chem_treat_method: - name: chem_treat_method - annotations: - Expected_value: - tag: Expected_value - value: measurement value;frequency;duration;duration - Preferred_unit: - tag: Preferred_unit - value: milligram per liter - description: Method of chemical administration(dose, frequency, duration, time - elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 - hr; 0 days) - title: chemical treatment method + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_symbiont_associated_data + multivalued: true + range: MigsViSymbiontAssociated + inlined: true + inlined_as_list: true + migs_vi_wastewater_sludge_data: + name: migs_vi_wastewater_sludge_data + description: Data that complies with MigsVi combined with WastewaterSludge + title: MigsViWastewaterSludge data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - method - - treatment - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}' - slot_uri: MIXS:0000457 - multivalued: false - required: false - recommended: false - chem_treatment: - name: chem_treatment - annotations: - Expected_value: - tag: Expected_value - value: name;name;timestamp - description: List of chemical compounds administered upstream the sampling location - where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, - demulsifiers, and other production chemicals etc.). The commercial name of the - product and name of the supplier should be provided. The date of administration - should also be included - title: chemical treatment - examples: - - value: ACCENT 1125;DOW;2010-11-17 + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_wastewater_sludge_data + multivalued: true + range: MigsViWastewaterSludge + inlined: true + inlined_as_list: true + migs_vi_water_data: + name: migs_vi_water_data + description: Data that complies with MigsVi combined with Water + title: MigsViWater data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - treatment - string_serialization: '{text};{text};{timestamp}' - slot_uri: MIXS:0001012 - multivalued: false - required: false - recommended: false - chimera_check: - name: chimera_check - description: Tool(s) used for chimera checking, including version number and parameters, - to discover and remove chimeric sequences. A chimeric sequence is comprised - of two or more phylogenetically distinct parent sequences - title: chimera check software - examples: - - value: uchime;v4.1;default parameters - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:migs_vi_water_data + multivalued: true + range: MigsViWater + inlined: true + inlined_as_list: true + mimag_data: + name: mimag_data + description: Data that complies with checklist Mimag + title: Mimag data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - software - slot_uri: MIXS:0000052 - multivalued: false - range: string - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{software};{version};{parameters}$ - interpolated: true - partial_match: true - chloride: - name: chloride - annotations: - Preferred_unit: - tag: Preferred_unit - value: milligram per liter, parts per million - description: Concentration of chloride in the sample - title: chloride - examples: - - value: 5000 milligram per liter + domain: MixsCompliantData + slot_uri: MIXS:mimag_data + multivalued: true + range: Mimag + inlined: true + inlined_as_list: true + mimag_agriculture_data: + name: mimag_agriculture_data + description: Data that complies with Mimag combined with Agriculture + title: MimagAgriculture data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000429 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - chlorophyll: - name: chlorophyll - annotations: - Preferred_unit: - tag: Preferred_unit - value: milligram per cubic meter, microgram per liter - description: Concentration of chlorophyll - title: chlorophyll - examples: - - value: 5 milligram per cubic meter + domain: MixsCompliantData + slot_uri: MIXS:mimag_agriculture_data + multivalued: true + range: MimagAgriculture + inlined: true + inlined_as_list: true + mimag_air_data: + name: mimag_air_data + description: Data that complies with Mimag combined with Air + title: MimagAir data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000177 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - climate_environment: - name: climate_environment - description: Treatment involving an exposure to a particular climate; treatment - regimen including how many times the treatment was repeated, how long each treatment - lasted, and the start and end time of the entire treatment; can include multiple - climates - title: climate environment - examples: - - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + domain: MixsCompliantData + slot_uri: MIXS:mimag_air_data + multivalued: true + range: MimagAir + inlined: true + inlined_as_list: true + mimag_built_environment_data: + name: mimag_built_environment_data + description: Data that complies with Mimag combined with BuiltEnvironment + title: MimagBuiltEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - environment - slot_uri: MIXS:0001040 + domain: MixsCompliantData + slot_uri: MIXS:mimag_built_environment_data multivalued: true - range: string - coll_site_geo_feat: - name: coll_site_geo_feat - annotations: - Expected_value: - tag: Expected_value - value: ENVO:00000002 or ENVO:00000070 - description: 'Text or terms that describe the geographic feature where the food - sample was obtained by the researcher. This field accepts selected terms listed - under the following ontologies: anthropogenic geographic feature (http://purl.obolibrary.org/obo/ENVO_00000002), - for example agricultural fairground [ENVO:01000986]; garden [ENVO:00000011} - or any of its subclasses; market [ENVO:01000987]; water well [ENVO:01000002]; - or human construction (http://purl.obolibrary.org/obo/ENVO_00000070)' - title: collection site geographic feature - examples: - - value: farm [ENVO:00000078] + range: MimagBuiltEnvironment + inlined: true + inlined_as_list: true + mimag_food_animal_and_animal_feed_data: + name: mimag_food_animal_and_animal_feed_data + description: Data that complies with Mimag combined with FoodAnimalAndAnimalFeed + title: MimagFoodAnimalAndAnimalFeed data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - feature - - geographic - - site - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001183 - multivalued: false - required: true - collection_date: - name: collection_date - description: 'The time of sampling, either as an instance (single point in time) - or interval. In case no exact time is available, the date/time can be right - truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; - 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant' - title: collection date - examples: - - value: '2013-03-25T12:42:31+01:00' - in_subset: - - environment + domain: MixsCompliantData + slot_uri: MIXS:mimag_food_animal_and_animal_feed_data + multivalued: true + range: MimagFoodAnimalAndAnimalFeed + inlined: true + inlined_as_list: true + mimag_food_farm_environment_data: + name: mimag_food_farm_environment_data + description: Data that complies with Mimag combined with FoodFarmEnvironment + title: MimagFoodFarmEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - date - slot_uri: MIXS:0000011 - multivalued: false - range: datetime - required: true - compl_appr: - name: compl_appr - annotations: - Expected_value: - tag: Expected_value - value: text - description: The approach used to determine the completeness of a given genomic - assembly, which would typically make use of a set of conserved marker genes - or a closely related reference genome. For UViG completeness, include reference - genome or group used, and contig feature suggesting a complete genome - title: completeness approach - examples: - - value: other - description: was other UViG length compared to the average length of - reference genomes from the P22virus genus (NCBI RefSeq v83) - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:mimag_food_farm_environment_data + multivalued: true + range: MimagFoodFarmEnvironment + inlined: true + inlined_as_list: true + mimag_food_food_production_facility_data: + name: mimag_food_food_production_facility_data + description: Data that complies with Mimag combined with FoodFoodProductionFacility + title: MimagFoodFoodProductionFacility data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000071 - range: COMPL_APPR_ENUM - compl_score: - name: compl_score - annotations: - Expected_value: - tag: Expected_value - value: quality;percent completeness - description: 'Completeness score is typically based on either the fraction of - markers found as compared to a database or the percent of a genome found as - compared to a closely related reference genome. High Quality Draft: >90%, Medium - Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated - completeness scores' - title: completeness score - examples: - - value: med;60% - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:mimag_food_food_production_facility_data + multivalued: true + range: MimagFoodFoodProductionFacility + inlined: true + inlined_as_list: true + mimag_food_human_foods_data: + name: mimag_food_human_foods_data + description: Data that complies with Mimag combined with FoodHumanFoods + title: MimagFoodHumanFoods data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - score - string_serialization: '[high|med|low];{percentage}' - slot_uri: MIXS:0000069 - multivalued: false - compl_software: - name: compl_software - annotations: - Expected_value: - tag: Expected_value - value: names and versions of software(s) used - description: Tools used for completion estimate, i.e. checkm, anvi'o, busco - title: completeness software - examples: - - value: checkm - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:mimag_food_human_foods_data + multivalued: true + range: MimagFoodHumanFoods + inlined: true + inlined_as_list: true + mimag_host_associated_data: + name: mimag_host_associated_data + description: Data that complies with Mimag combined with HostAssociated + title: MimagHostAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - software - string_serialization: '{software};{version}' - slot_uri: MIXS:0000070 - multivalued: false - conduc: - name: conduc - annotations: - Preferred_unit: - tag: Preferred_unit - value: milliSiemens per centimeter - description: Electrical conductivity of water - title: conductivity - examples: - - value: 10 milliSiemens per centimeter + domain: MixsCompliantData + slot_uri: MIXS:mimag_host_associated_data + multivalued: true + range: MimagHostAssociated + inlined: true + inlined_as_list: true + mimag_human_associated_data: + name: mimag_human_associated_data + description: Data that complies with Mimag combined with HumanAssociated + title: MimagHumanAssociated data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000692 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - cons_food_stor_dur: - name: cons_food_stor_dur - annotations: - Preferred_unit: - tag: Preferred_unit - value: hours or days - description: The storage duration of the food commodity by the consumer, prior - to onset of illness or sample collection. Indicate the timepoint written in - ISO 8601 format - title: food stored by consumer (storage duration) - examples: - - value: P5D + domain: MixsCompliantData + slot_uri: MIXS:mimag_human_associated_data + multivalued: true + range: MimagHumanAssociated + inlined: true + inlined_as_list: true + mimag_human_gut_data: + name: mimag_human_gut_data + description: Data that complies with Mimag combined with HumanGut + title: MimagHumanGut data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - consumer - - duration) - - food - - storage - slot_uri: MIXS:0001195 - multivalued: false - range: string - required: false - recommended: false - pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ - structured_pattern: - syntax: ^{duration}$ - interpolated: true - partial_match: true - cons_food_stor_temp: - name: cons_food_stor_temp - annotations: - Expected_value: - tag: Expected_value - value: text or measurement value - Preferred_unit: - tag: Preferred_unit - value: degree Celsius - description: Temperature at which food commodity was stored by the consumer, prior - to onset of illness or sample collection - title: food stored by consumer (storage temperature) - examples: - - value: 4 degree Celsius + domain: MixsCompliantData + slot_uri: MIXS:mimag_human_gut_data + multivalued: true + range: MimagHumanGut + inlined: true + inlined_as_list: true + mimag_human_oral_data: + name: mimag_human_oral_data + description: Data that complies with Mimag combined with HumanOral + title: MimagHumanOral data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - consumer - - food - - storage - - temperature - string_serialization: '{float} {unit}|{text}' - slot_uri: MIXS:0001196 - multivalued: false - required: false - recommended: false - cons_purch_date: - name: cons_purch_date - description: The date a food product was purchased by consumer - title: purchase date - examples: - - value: '2013-03-25T12:42:31+01:00' + domain: MixsCompliantData + slot_uri: MIXS:mimag_human_oral_data + multivalued: true + range: MimagHumanOral + inlined: true + inlined_as_list: true + mimag_human_skin_data: + name: mimag_human_skin_data + description: Data that complies with Mimag combined with HumanSkin + title: MimagHumanSkin data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - date - slot_uri: MIXS:0001197 - multivalued: false - range: datetime - required: false - recommended: false - cons_qty_purchased: - name: cons_qty_purchased - description: The quantity of food purchased by consumer - title: quantity purchased - examples: - - value: 5 cans + domain: MixsCompliantData + slot_uri: MIXS:mimag_human_skin_data + multivalued: true + range: MimagHumanSkin + inlined: true + inlined_as_list: true + mimag_human_vaginal_data: + name: mimag_human_vaginal_data + description: Data that complies with Mimag combined with HumanVaginal + title: MimagHumanVaginal data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - quantity - slot_uri: MIXS:0001198 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{integer} {text}$ - interpolated: true - partial_match: true - contam_score: - name: contam_score - description: 'The contamination score is based on the fraction of single-copy - genes that are observed more than once in a query genome. The following scores - are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low - Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be - deposited into any of the public databases' - title: contamination score - examples: - - value: '0.01' - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:mimag_human_vaginal_data + multivalued: true + range: MimagHumanVaginal + inlined: true + inlined_as_list: true + mimag_hydrocarbon_resources_cores_data: + name: mimag_hydrocarbon_resources_cores_data + description: Data that complies with Mimag combined with HydrocarbonResourcesCores + title: MimagHydrocarbonResourcesCores data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - score - slot_uri: MIXS:0000072 - multivalued: false - range: float - contam_screen_input: - name: contam_screen_input - description: The type of sequence data used as input - title: contamination screening input - examples: - - value: contigs - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:mimag_hydrocarbon_resources_cores_data + multivalued: true + range: MimagHydrocarbonResourcesCores + inlined: true + inlined_as_list: true + mimag_hydrocarbon_resources_fluids_swabs_data: + name: mimag_hydrocarbon_resources_fluids_swabs_data + description: Data that complies with Mimag combined with HydrocarbonResourcesFluidsSwabs + title: MimagHydrocarbonResourcesFluidsSwabs data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000005 - multivalued: false - range: CONTAM_SCREEN_INPUT_ENUM - contam_screen_param: - name: contam_screen_param - annotations: - Expected_value: - tag: Expected_value - value: enumeration;value or name - description: Specific parameters used in the decontamination sofware, such as - reference database, coverage, and kmers. Combinations of these parameters may - also be used, i.e. kmer and coverage, or reference database and kmer - title: contamination screening parameters - examples: - - value: kmer - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:mimag_hydrocarbon_resources_fluids_swabs_data + multivalued: true + range: MimagHydrocarbonResourcesFluidsSwabs + inlined: true + inlined_as_list: true + mimag_microbial_mat_biofilm_data: + name: mimag_microbial_mat_biofilm_data + description: Data that complies with Mimag combined with MicrobialMatBiofilm + title: MimagMicrobialMatBiofilm data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - parameter - string_serialization: '[ref db|kmer|coverage|combination];{text|integer}' - slot_uri: MIXS:0000073 - multivalued: false - cool_syst_id: - name: cool_syst_id - description: The cooling system identifier - title: cooling system identifier - examples: - - value: '12345' + domain: MixsCompliantData + slot_uri: MIXS:mimag_microbial_mat_biofilm_data + multivalued: true + range: MimagMicrobialMatBiofilm + inlined: true + inlined_as_list: true + mimag_miscellaneous_natural_or_artificial_environment_data: + name: mimag_miscellaneous_natural_or_artificial_environment_data + description: Data that complies with Mimag combined with MiscellaneousNaturalOrArtificialEnvironment + title: MimagMiscellaneousNaturalOrArtificialEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - identifier - slot_uri: MIXS:0000785 - multivalued: false - range: integer - required: false - recommended: false - crop_rotation: - name: crop_rotation - annotations: - Expected_value: - tag: Expected_value - value: crop rotation status;schedule - description: Whether or not crop is rotated, and if yes, rotation schedule - title: history/crop rotation - examples: - - value: yes;R2/2017-01-01/2018-12-31/P6M + domain: MixsCompliantData + slot_uri: MIXS:mimag_miscellaneous_natural_or_artificial_environment_data + multivalued: true + range: MimagMiscellaneousNaturalOrArtificialEnvironment + inlined: true + inlined_as_list: true + mimag_plant_associated_data: + name: mimag_plant_associated_data + description: Data that complies with Mimag combined with PlantAssociated + title: MimagPlantAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - history - slot_uri: MIXS:0000318 - multivalued: false - crop_yield: - name: crop_yield - annotations: - Preferred_unit: - tag: Preferred_unit - value: kilogram per metre square - description: Amount of crop produced per unit or area of land - title: crop yield - examples: - - value: 570 kilogram per metre square + domain: MixsCompliantData + slot_uri: MIXS:mimag_plant_associated_data + multivalued: true + range: MimagPlantAssociated + inlined: true + inlined_as_list: true + mimag_sediment_data: + name: mimag_sediment_data + description: Data that complies with Mimag combined with Sediment + title: MimagSediment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - crop - slot_uri: MIXS:0001116 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - cult_isol_date: - name: cult_isol_date - description: The datetime marking the end of a process in which a sample yields - a positive result for the target microbial analyte(s) in the form of an isolated - colony or colonies - title: culture isolation date - examples: - - value: '2018-05-11T10:00:00+01:00' + domain: MixsCompliantData + slot_uri: MIXS:mimag_sediment_data + multivalued: true + range: MimagSediment + inlined: true + inlined_as_list: true + mimag_soil_data: + name: mimag_soil_data + description: Data that complies with Mimag combined with Soil + title: MimagSoil data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - culture - - date - - isolation - slot_uri: MIXS:0001181 - multivalued: false - range: datetime - required: false - recommended: false - cult_result: - name: cult_result - description: Any result of a bacterial culture experiment reported as a binary - assessment such as positive/negative, active/inactive - title: culture result - examples: - - value: positive + domain: MixsCompliantData + slot_uri: MIXS:mimag_soil_data + multivalued: true + range: MimagSoil + inlined: true + inlined_as_list: true + mimag_symbiont_associated_data: + name: mimag_symbiont_associated_data + description: Data that complies with Mimag combined with SymbiontAssociated + title: MimagSymbiontAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - culture - slot_uri: MIXS:0001117 - multivalued: false - range: CULT_RESULT_ENUM - required: false - recommended: false - cult_result_org: - name: cult_result_org - description: Taxonomic information about the cultured organism(s) - title: culture result organism - examples: - - value: Listeria monocytogenes [NCIT:C86502] + domain: MixsCompliantData + slot_uri: MIXS:mimag_symbiont_associated_data + multivalued: true + range: MimagSymbiontAssociated + inlined: true + inlined_as_list: true + mimag_wastewater_sludge_data: + name: mimag_wastewater_sludge_data + description: Data that complies with Mimag combined with WastewaterSludge + title: MimagWastewaterSludge data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - culture - - organism - slot_uri: MIXS:0001118 + domain: MixsCompliantData + slot_uri: MIXS:mimag_wastewater_sludge_data multivalued: true - range: string - required: false - recommended: false - pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ - structured_pattern: - syntax: ^({termLabel} \[{termID}\])|{integer}$ - interpolated: true - partial_match: true - cult_root_med: - name: cult_root_med - annotations: - Expected_value: - tag: Expected_value - value: name, PMID,DOI or url - description: Name or reference for the hydroponic or in vitro culture rooting - medium; can be the name of a commonly used medium or reference to a specific - medium, e.g. Murashige and Skoog medium. If the medium has not been formally - published, use the rooting medium descriptors - title: culture rooting medium - examples: - - value: http://himedialabs.com/TD/PT158.pdf + range: MimagWastewaterSludge + inlined: true + inlined_as_list: true + mimag_water_data: + name: mimag_water_data + description: Data that complies with Mimag combined with Water + title: MimagWater data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - culture - string_serialization: '{text}|{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0001041 - multivalued: false - required: false - recommended: false - cult_target: - name: cult_target - annotations: - Expected_value: - tag: Expected_value - value: NCIT:C14250 or NCBI taxid or culture independent - description: The target microbial analyte in terms of investigation scope. This - field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). - This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy - title: culture target microbial analyte - examples: - - value: Listeria monocytogenes [NCIT:C86502] + domain: MixsCompliantData + slot_uri: MIXS:mimag_water_data + multivalued: true + range: MimagWater + inlined: true + inlined_as_list: true + mimarks_c_data: + name: mimarks_c_data + description: Data that complies with checklist MimarksC + title: MimarksC data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - culture - - microbial - - target - string_serialization: '{termLabel} [{termID}]|{integer}' - slot_uri: MIXS:0001119 + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_data multivalued: true - required: false - recommended: false - cur_land_use: - name: cur_land_use - annotations: - Expected_value: - tag: Expected_value - value: enumeration - description: Present state of sample site - title: current land use - examples: - - value: conifers + range: MimarksC + inlined: true + inlined_as_list: true + mimarks_c_agriculture_data: + name: mimarks_c_agriculture_data + description: Data that complies with MimarksC combined with Agriculture + title: MimarksCAgriculture data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - land - - use - string_serialization: '[cities|farmstead|industrial areas|roads/railroads|rock|sand|gravel|mudflats|salt - flats|badlands|permanent snow or ice|saline seeps|mines/quarries|oil waste areas|small - grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands - (grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands - used for livestock grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub - land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)|successional - shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub - crops (blueberries,nursery ornamentals,filberts)|vine crops (grapes)|conifers - (e.g. pine,spruce,fir,cypress)|hardwoods (e.g. oak,hickory,elm,aspen)|intermixed - hardwood and conifers|tropical (e.g. mangrove,palms)|rainforest (evergreen forest - receiving >406 cm annual rainfall)|swamp (permanent or semi-permanent water - body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery - trees)]' - slot_uri: MIXS:0001080 - multivalued: false - required: false - recommended: false - cur_vegetation: - name: cur_vegetation - annotations: - Expected_value: - tag: Expected_value - value: current vegetation type - description: Vegetation classification from one or more standard classification - systems, or agricultural crop - title: current vegetation + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_agriculture_data + multivalued: true + range: MimarksCAgriculture + inlined: true + inlined_as_list: true + mimarks_c_air_data: + name: mimarks_c_air_data + description: Data that complies with MimarksC combined with Air + title: MimarksCAir data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - vegetation - string_serialization: '{text}' - slot_uri: MIXS:0000312 - multivalued: false - cur_vegetation_meth: - name: cur_vegetation_meth - description: Reference or method used in vegetation classification - title: current vegetation method + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_air_data + multivalued: true + range: MimarksCAir + inlined: true + inlined_as_list: true + mimarks_c_built_environment_data: + name: mimarks_c_built_environment_data + description: Data that complies with MimarksC combined with BuiltEnvironment + title: MimarksCBuiltEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - method - - vegetation - slot_uri: MIXS:0000314 - multivalued: false - range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ - structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ - interpolated: true - partial_match: true - date_extr_weath: - name: date_extr_weath - description: Date of unusual weather events that may have affected microbial populations. - Multiple terms can be separated by pipes, listed in reverse chronological order - title: extreme weather date - examples: - - value: '2013-03-25T12:42:31+01:00' + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_built_environment_data + multivalued: true + range: MimarksCBuiltEnvironment + inlined: true + inlined_as_list: true + mimarks_c_food_animal_and_animal_feed_data: + name: mimarks_c_food_animal_and_animal_feed_data + description: Data that complies with MimarksC combined with FoodAnimalAndAnimalFeed + title: MimarksCFoodAnimalAndAnimalFeed data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - date - - extreme - - weather - slot_uri: MIXS:0001142 + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_food_animal_and_animal_feed_data multivalued: true - range: datetime - required: false - recommended: false - date_last_rain: - name: date_last_rain - description: The date of the last time it rained - title: date last rain - examples: - - value: '2013-03-25T12:42:31+01:00' + range: MimarksCFoodAnimalAndAnimalFeed + inlined: true + inlined_as_list: true + mimarks_c_food_farm_environment_data: + name: mimarks_c_food_farm_environment_data + description: Data that complies with MimarksC combined with FoodFarmEnvironment + title: MimarksCFoodFarmEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - date - - rain - slot_uri: MIXS:0000786 - multivalued: false - range: datetime - required: false - recommended: false - decontam_software: - name: decontam_software - annotations: - Expected_value: - tag: Expected_value - value: enumeration - description: Tool(s) used in contamination screening - title: decontamination software - examples: - - value: anvi'o - in_subset: - - sequencing - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - software - string_serialization: '[checkm/refinem|anvi''o|prodege|bbtools:decontaminate.sh|acdc|combination]' - slot_uri: MIXS:0000074 - multivalued: false - density: - name: density - annotations: - Preferred_unit: - tag: Preferred_unit - value: gram per cubic meter, gram per cubic centimeter - description: Density of the sample, which is its mass per unit volume (aka volumetric - mass density) - title: density - examples: - - value: 1000 kilogram per cubic meter + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_food_farm_environment_data + multivalued: true + range: MimarksCFoodFarmEnvironment + inlined: true + inlined_as_list: true + mimarks_c_food_food_production_facility_data: + name: mimarks_c_food_food_production_facility_data + description: Data that complies with MimarksC combined with FoodFoodProductionFacility + title: MimarksCFoodFoodProductionFacility data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - density - slot_uri: MIXS:0000435 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - depos_env: - name: depos_env - description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). - If "other" is specified, please propose entry in "additional info" field - title: depositional environment + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_food_food_production_facility_data + multivalued: true + range: MimarksCFoodFoodProductionFacility + inlined: true + inlined_as_list: true + mimarks_c_food_human_foods_data: + name: mimarks_c_food_human_foods_data + description: Data that complies with MimarksC combined with FoodHumanFoods + title: MimarksCFoodHumanFoods data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - environment - slot_uri: MIXS:0000992 - multivalued: false - range: DEPOS_ENV_ENUM - recommended: true - depth: - name: depth - annotations: - Preferred_unit: - tag: Preferred_unit - value: meter - description: The vertical distance below local surface. For sediment or soil samples - depth is measured from sediment or soil surface, respectively. Depth can be - reported as an interval for subsurface samples - title: depth - in_subset: - - environment + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_food_human_foods_data + multivalued: true + range: MimarksCFoodHumanFoods + inlined: true + inlined_as_list: true + mimarks_c_host_associated_data: + name: mimarks_c_host_associated_data + description: Data that complies with MimarksC combined with HostAssociated + title: MimarksCHostAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - depth - slot_uri: MIXS:0000018 - multivalued: false - range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - dermatology_disord: - name: dermatology_disord - description: History of dermatology disorders; can include multiple disorders. - The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - skin disease (https://disease-ontology.org/?id=DOID:37) - title: dermatology disorder + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_host_associated_data + multivalued: true + range: MimarksCHostAssociated + inlined: true + inlined_as_list: true + mimarks_c_human_associated_data: + name: mimarks_c_human_associated_data + description: Data that complies with MimarksC combined with HumanAssociated + title: MimarksCHumanAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - disorder - slot_uri: MIXS:0000284 + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_human_associated_data multivalued: true - range: string - required: false - recommended: false - detec_type: - name: detec_type - annotations: - Expected_value: - tag: Expected_value - value: enumeration - description: Type of UViG detection - title: detection type - examples: - - value: independent sequence (UViG) - in_subset: - - sequencing + range: MimarksCHumanAssociated + inlined: true + inlined_as_list: true + mimarks_c_human_gut_data: + name: mimarks_c_human_gut_data + description: Data that complies with MimarksC combined with HumanGut + title: MimarksCHumanGut data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - type - string_serialization: '[independent sequence (UViG)|provirus (UpViG)]' - slot_uri: MIXS:0000084 - multivalued: false - dew_point: - name: dew_point - annotations: - Preferred_unit: - tag: Preferred_unit - value: degree Celsius - description: The temperature to which a given parcel of humid air must be cooled, - at constant barometric pressure, for water vapor to condense into water - title: dew point - examples: - - value: 22 degree Celsius + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_human_gut_data + multivalued: true + range: MimarksCHumanGut + inlined: true + inlined_as_list: true + mimarks_c_human_oral_data: + name: mimarks_c_human_oral_data + description: Data that complies with MimarksC combined with HumanOral + title: MimarksCHumanOral data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000129 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - diet_last_six_month: - name: diet_last_six_month - annotations: - Expected_value: - tag: Expected_value - value: diet change;current diet - description: Specification of major diet changes in the last six months, if yes - the change should be specified - title: major diet change in last six months - examples: - - value: yes;vegetarian diet + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_human_oral_data + multivalued: true + range: MimarksCHumanOral + inlined: true + inlined_as_list: true + mimarks_c_human_skin_data: + name: mimarks_c_human_skin_data + description: Data that complies with MimarksC combined with HumanSkin + title: MimarksCHumanSkin data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - diet - - months - string_serialization: '{boolean};{text}' - slot_uri: MIXS:0000266 - multivalued: false - required: false - recommended: false - dietary_claim_use: - name: dietary_claim_use - annotations: - Expected_value: - tag: Expected_value - value: FOODON:03510023 - description: These descriptors are used either for foods intended for special - dietary use as defined in 21 CFR 105 or for foods that have special characteristics - indicated in the name or labeling. This field accepts terms listed under dietary - claim or use (http://purl.obolibrary.org/obo/FOODON_03510023). Multiple terms - can be separated by one or more pipes, but please consider limiting this list - to the most prominent dietary claim or use - title: dietary claim or use - examples: - - value: No preservatives [FOODON:03510113] + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_human_skin_data + multivalued: true + range: MimarksCHumanSkin + inlined: true + inlined_as_list: true + mimarks_c_human_vaginal_data: + name: mimarks_c_human_vaginal_data + description: Data that complies with MimarksC combined with HumanVaginal + title: MimarksCHumanVaginal data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - diet - - use - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001199 + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_human_vaginal_data multivalued: true - required: false - recommended: false - diether_lipids: - name: diether_lipids - annotations: - Expected_value: - tag: Expected_value - value: diether lipid name;measurement value - Preferred_unit: - tag: Preferred_unit - value: nanogram per liter - description: Concentration of diether lipids; can include multiple types of diether - lipids - title: diether lipids - examples: - - value: 0.2 nanogram per liter + range: MimarksCHumanVaginal + inlined: true + inlined_as_list: true + mimarks_c_hydrocarbon_resources_cores_data: + name: mimarks_c_hydrocarbon_resources_cores_data + description: Data that complies with MimarksC combined with HydrocarbonResourcesCores + title: MimarksCHydrocarbonResourcesCores data from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000178 + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_hydrocarbon_resources_cores_data multivalued: true - required: false - recommended: false - diss_carb_dioxide: - name: diss_carb_dioxide - annotations: - Preferred_unit: - tag: Preferred_unit - value: micromole per liter, milligram per liter - description: Concentration of dissolved carbon dioxide in the sample or liquid - portion of the sample - title: dissolved carbon dioxide - examples: - - value: 5 milligram per liter + range: MimarksCHydrocarbonResourcesCores + inlined: true + inlined_as_list: true + mimarks_c_hydrocarbon_resources_fluids_swabs_data: + name: mimarks_c_hydrocarbon_resources_fluids_swabs_data + description: Data that complies with MimarksC combined with HydrocarbonResourcesFluidsSwabs + title: MimarksCHydrocarbonResourcesFluidsSwabs data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - carbon - - dissolved - slot_uri: MIXS:0000436 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - diss_hydrogen: - name: diss_hydrogen - annotations: - Preferred_unit: - tag: Preferred_unit - value: micromole per liter - description: Concentration of dissolved hydrogen - title: dissolved hydrogen - examples: - - value: 0.3 micromole per liter + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_hydrocarbon_resources_fluids_swabs_data + multivalued: true + range: MimarksCHydrocarbonResourcesFluidsSwabs + inlined: true + inlined_as_list: true + mimarks_c_microbial_mat_biofilm_data: + name: mimarks_c_microbial_mat_biofilm_data + description: Data that complies with MimarksC combined with MicrobialMatBiofilm + title: MimarksCMicrobialMatBiofilm data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - dissolved - slot_uri: MIXS:0000179 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - diss_inorg_carb: - name: diss_inorg_carb - annotations: - Preferred_unit: - tag: Preferred_unit - value: microgram per liter, milligram per liter, parts per million - description: Dissolved inorganic carbon concentration in the sample, typically - measured after filtering the sample using a 0.45 micrometer filter - title: dissolved inorganic carbon - examples: - - value: 2059 micromole per kilogram + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_microbial_mat_biofilm_data + multivalued: true + range: MimarksCMicrobialMatBiofilm + inlined: true + inlined_as_list: true + mimarks_c_miscellaneous_natural_or_artificial_environment_data: + name: mimarks_c_miscellaneous_natural_or_artificial_environment_data + description: Data that complies with MimarksC combined with MiscellaneousNaturalOrArtificialEnvironment + title: MimarksCMiscellaneousNaturalOrArtificialEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - carbon - - dissolved - - inorganic - slot_uri: MIXS:0000434 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - diss_inorg_nitro: - name: diss_inorg_nitro - annotations: - Preferred_unit: - tag: Preferred_unit - value: microgram per liter, micromole per liter - description: Concentration of dissolved inorganic nitrogen - title: dissolved inorganic nitrogen - examples: - - value: 761 micromole per liter + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_miscellaneous_natural_or_artificial_environment_data + multivalued: true + range: MimarksCMiscellaneousNaturalOrArtificialEnvironment + inlined: true + inlined_as_list: true + mimarks_c_plant_associated_data: + name: mimarks_c_plant_associated_data + description: Data that complies with MimarksC combined with PlantAssociated + title: MimarksCPlantAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - dissolved - - inorganic - - nitrogen - slot_uri: MIXS:0000698 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - diss_inorg_phosp: - name: diss_inorg_phosp - description: Concentration of dissolved inorganic phosphorus in the sample - title: dissolved inorganic phosphorus - examples: - - value: 56.5 micromole per liter + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_plant_associated_data + multivalued: true + range: MimarksCPlantAssociated + inlined: true + inlined_as_list: true + mimarks_c_sediment_data: + name: mimarks_c_sediment_data + description: Data that complies with MimarksC combined with Sediment + title: MimarksCSediment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - dissolved - - inorganic - - phosphorus - slot_uri: MIXS:0000106 - multivalued: false - range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - diss_iron: - name: diss_iron - annotations: - Preferred_unit: - tag: Preferred_unit - value: milligram per liter - description: Concentration of dissolved iron in the sample - title: dissolved iron + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_sediment_data + multivalued: true + range: MimarksCSediment + inlined: true + inlined_as_list: true + mimarks_c_soil_data: + name: mimarks_c_soil_data + description: Data that complies with MimarksC combined with Soil + title: MimarksCSoil data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - dissolved - slot_uri: MIXS:0000139 - multivalued: false - range: string - recommended: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - diss_org_carb: - name: diss_org_carb - annotations: - Preferred_unit: - tag: Preferred_unit - value: micromole per liter, milligram per liter - description: Concentration of dissolved organic carbon in the sample, liquid portion - of the sample, or aqueous phase of the fluid - title: dissolved organic carbon - examples: - - value: 197 micromole per liter + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_soil_data + multivalued: true + range: MimarksCSoil + inlined: true + inlined_as_list: true + mimarks_c_symbiont_associated_data: + name: mimarks_c_symbiont_associated_data + description: Data that complies with MimarksC combined with SymbiontAssociated + title: MimarksCSymbiontAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - carbon - - dissolved - - organic - slot_uri: MIXS:0000433 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - diss_org_nitro: - name: diss_org_nitro - description: Dissolved organic nitrogen concentration measured as; total dissolved - nitrogen - NH4 - NO3 - NO2 - title: dissolved organic nitrogen - examples: - - value: 0.05 micromole per liter + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_symbiont_associated_data + multivalued: true + range: MimarksCSymbiontAssociated + inlined: true + inlined_as_list: true + mimarks_c_wastewater_sludge_data: + name: mimarks_c_wastewater_sludge_data + description: Data that complies with MimarksC combined with WastewaterSludge + title: MimarksCWastewaterSludge data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - dissolved - - nitrogen - - organic - slot_uri: MIXS:0000162 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - diss_oxygen: - name: diss_oxygen - annotations: - Preferred_unit: - tag: Preferred_unit - value: micromole per kilogram, milligram per liter - description: Concentration of dissolved oxygen - title: dissolved oxygen - examples: - - value: 175 micromole per kilogram + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_wastewater_sludge_data + multivalued: true + range: MimarksCWastewaterSludge + inlined: true + inlined_as_list: true + mimarks_c_water_data: + name: mimarks_c_water_data + description: Data that complies with MimarksC combined with Water + title: MimarksCWater data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - dissolved - - oxygen - slot_uri: MIXS:0000119 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - diss_oxygen_fluid: - name: diss_oxygen_fluid - annotations: - Preferred_unit: - tag: Preferred_unit - value: micromole per kilogram, milligram per liter - description: Concentration of dissolved oxygen in the oil field produced fluids - as it contributes to oxgen-corrosion and microbial activity (e.g. Mic) - title: dissolved oxygen in fluids + domain: MixsCompliantData + slot_uri: MIXS:mimarks_c_water_data + multivalued: true + range: MimarksCWater + inlined: true + inlined_as_list: true + mimarks_s_data: + name: mimarks_s_data + description: Data that complies with checklist MimarksS + title: MimarksS data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - dissolved - - oxygen - slot_uri: MIXS:0000438 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - dominant_hand: - name: dominant_hand - description: Dominant hand of the subject - title: dominant hand - examples: - - value: right + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_data + multivalued: true + range: MimarksS + inlined: true + inlined_as_list: true + mimarks_s_agriculture_data: + name: mimarks_s_agriculture_data + description: Data that complies with MimarksS combined with Agriculture + title: MimarksSAgriculture data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000944 - multivalued: false - range: DOMINANT_HAND_ENUM - required: false - recommended: false - door_comp_type: - name: door_comp_type - description: The composite type of the door - title: door type, composite - examples: - - value: revolving + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_agriculture_data + multivalued: true + range: MimarksSAgriculture + inlined: true + inlined_as_list: true + mimarks_s_air_data: + name: mimarks_s_air_data + description: Data that complies with MimarksS combined with Air + title: MimarksSAir data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - door - - type - slot_uri: MIXS:0000795 - multivalued: false - range: DOOR_COMP_TYPE_ENUM - required: false - recommended: false - door_cond: - name: door_cond - description: The phsical condition of the door - title: door condition - examples: - - value: new + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_air_data + multivalued: true + range: MimarksSAir + inlined: true + inlined_as_list: true + mimarks_s_built_environment_data: + name: mimarks_s_built_environment_data + description: Data that complies with MimarksS combined with BuiltEnvironment + title: MimarksSBuiltEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - condition - - door - slot_uri: MIXS:0000788 - multivalued: false - range: SHARED_ENUM_2 - required: false - recommended: false - door_direct: - name: door_direct - description: The direction the door opens - title: door direction of opening - examples: - - value: inward + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_built_environment_data + multivalued: true + range: MimarksSBuiltEnvironment + inlined: true + inlined_as_list: true + mimarks_s_food_animal_and_animal_feed_data: + name: mimarks_s_food_animal_and_animal_feed_data + description: Data that complies with MimarksS combined with FoodAnimalAndAnimalFeed + title: MimarksSFoodAnimalAndAnimalFeed data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - direction - - door - slot_uri: MIXS:0000789 - multivalued: false - range: DOOR_DIRECT_ENUM - required: false - recommended: false - door_loc: - name: door_loc - description: The relative location of the door in the room - title: door location - examples: - - value: north + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_food_animal_and_animal_feed_data + multivalued: true + range: MimarksSFoodAnimalAndAnimalFeed + inlined: true + inlined_as_list: true + mimarks_s_food_farm_environment_data: + name: mimarks_s_food_farm_environment_data + description: Data that complies with MimarksS combined with FoodFarmEnvironment + title: MimarksSFoodFarmEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - door - - location - slot_uri: MIXS:0000790 - multivalued: false - range: SHARED_ENUM_0 - required: false - recommended: false - door_mat: - name: door_mat - description: The material the door is composed of - title: door material - examples: - - value: wood + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_food_farm_environment_data + multivalued: true + range: MimarksSFoodFarmEnvironment + inlined: true + inlined_as_list: true + mimarks_s_food_food_production_facility_data: + name: mimarks_s_food_food_production_facility_data + description: Data that complies with MimarksS combined with FoodFoodProductionFacility + title: MimarksSFoodFoodProductionFacility data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - door - - material - slot_uri: MIXS:0000791 - multivalued: false - range: DOOR_MAT_ENUM - required: false - recommended: false - door_move: - name: door_move - description: The type of movement of the door - title: door movement - examples: - - value: swinging + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_food_food_production_facility_data + multivalued: true + range: MimarksSFoodFoodProductionFacility + inlined: true + inlined_as_list: true + mimarks_s_food_human_foods_data: + name: mimarks_s_food_human_foods_data + description: Data that complies with MimarksS combined with FoodHumanFoods + title: MimarksSFoodHumanFoods data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - door - slot_uri: MIXS:0000792 - multivalued: false - range: DOOR_MOVE_ENUM - required: false - recommended: false - door_size: - name: door_size - annotations: - Preferred_unit: - tag: Preferred_unit - value: square meter - description: The size of the door - title: door area or size - examples: - - value: 2.5 square meter + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_food_human_foods_data + multivalued: true + range: MimarksSFoodHumanFoods + inlined: true + inlined_as_list: true + mimarks_s_host_associated_data: + name: mimarks_s_host_associated_data + description: Data that complies with MimarksS combined with HostAssociated + title: MimarksSHostAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - area - - door - - size - slot_uri: MIXS:0000158 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - door_type: - name: door_type - description: The type of door material - title: door type - examples: - - value: wooden + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_host_associated_data + multivalued: true + range: MimarksSHostAssociated + inlined: true + inlined_as_list: true + mimarks_s_human_associated_data: + name: mimarks_s_human_associated_data + description: Data that complies with MimarksS combined with HumanAssociated + title: MimarksSHumanAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - door - - type - slot_uri: MIXS:0000794 - multivalued: false - range: DOOR_TYPE_ENUM - required: false - recommended: false - door_type_metal: - name: door_type_metal - description: The type of metal door - title: door type, metal - examples: - - value: hollow + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_human_associated_data + multivalued: true + range: MimarksSHumanAssociated + inlined: true + inlined_as_list: true + mimarks_s_human_gut_data: + name: mimarks_s_human_gut_data + description: Data that complies with MimarksS combined with HumanGut + title: MimarksSHumanGut data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - door - - type - slot_uri: MIXS:0000796 - multivalued: false - range: DOOR_TYPE_METAL_ENUM - required: false - recommended: false - door_type_wood: - name: door_type_wood - annotations: - Expected_value: - tag: Expected_value - value: enumeration - description: The type of wood door - title: door type, wood - examples: - - value: battened + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_human_gut_data + multivalued: true + range: MimarksSHumanGut + inlined: true + inlined_as_list: true + mimarks_s_human_oral_data: + name: mimarks_s_human_oral_data + description: Data that complies with MimarksS combined with HumanOral + title: MimarksSHumanOral data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - door - - type - string_serialization: '[bettened and ledged|battened|ledged and braced|battened|ledged - and framed|battened|ledged, braced and frame|framed and paneled|glashed or sash|flush|louvered|wire - gauged]' - slot_uri: MIXS:0000797 - multivalued: false - required: false - recommended: false - door_water_mold: - name: door_water_mold - description: Signs of the presence of mold or mildew on a door - title: door signs of water/mold - examples: - - value: presence of mold visible + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_human_oral_data + multivalued: true + range: MimarksSHumanOral + inlined: true + inlined_as_list: true + mimarks_s_human_skin_data: + name: mimarks_s_human_skin_data + description: Data that complies with MimarksS combined with HumanSkin + title: MimarksSHumanSkin data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - door - slot_uri: MIXS:0000793 - multivalued: false - range: SHARED_ENUM_1 - required: false - recommended: false - douche: - name: douche - description: Date of most recent douche - title: douche - examples: - - value: '2013-03-25T12:42:31+01:00' + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_human_skin_data + multivalued: true + range: MimarksSHumanSkin + inlined: true + inlined_as_list: true + mimarks_s_human_vaginal_data: + name: mimarks_s_human_vaginal_data + description: Data that complies with MimarksS combined with HumanVaginal + title: MimarksSHumanVaginal data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000967 - multivalued: false - range: datetime - required: false - recommended: false - down_par: - name: down_par - annotations: - Preferred_unit: - tag: Preferred_unit - value: microEinstein per square meter per second, microEinstein per square - centimeter per second - description: Visible waveband radiance and irradiance measurements in the water - column - title: downward PAR - examples: - - value: 28.71 microEinstein per square meter per second + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_human_vaginal_data + multivalued: true + range: MimarksSHumanVaginal + inlined: true + inlined_as_list: true + mimarks_s_hydrocarbon_resources_cores_data: + name: mimarks_s_hydrocarbon_resources_cores_data + description: Data that complies with MimarksS combined with HydrocarbonResourcesCores + title: MimarksSHydrocarbonResourcesCores data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000703 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - drainage_class: - name: drainage_class - description: Drainage classification from a standard system such as the USDA system - title: drainage classification - examples: - - value: well + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_hydrocarbon_resources_cores_data + multivalued: true + range: MimarksSHydrocarbonResourcesCores + inlined: true + inlined_as_list: true + mimarks_s_hydrocarbon_resources_fluids_swabs_data: + name: mimarks_s_hydrocarbon_resources_fluids_swabs_data + description: Data that complies with MimarksS combined with HydrocarbonResourcesFluidsSwabs + title: MimarksSHydrocarbonResourcesFluidsSwabs data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - classification - slot_uri: MIXS:0001085 - multivalued: false - range: DRAINAGE_CLASS_ENUM - drawings: - name: drawings - description: The buildings architectural drawings; if design is chosen, indicate - phase-conceptual, schematic, design development, and construction documents - title: drawings - examples: - - value: sketch + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_hydrocarbon_resources_fluids_swabs_data + multivalued: true + range: MimarksSHydrocarbonResourcesFluidsSwabs + inlined: true + inlined_as_list: true + mimarks_s_microbial_mat_biofilm_data: + name: mimarks_s_microbial_mat_biofilm_data + description: Data that complies with MimarksS combined with MicrobialMatBiofilm + title: MimarksSMicrobialMatBiofilm data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - drawings - slot_uri: MIXS:0000798 - multivalued: false - range: DRAWINGS_ENUM - required: false - recommended: false - drug_usage: - name: drug_usage - annotations: - Expected_value: - tag: Expected_value - value: drug name;frequency - description: Any drug used by subject and the frequency of usage; can include - multiple drugs used - title: drug usage - examples: - - value: Lipitor;2/day + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_microbial_mat_biofilm_data + multivalued: true + range: MimarksSMicrobialMatBiofilm + inlined: true + inlined_as_list: true + mimarks_s_miscellaneous_natural_or_artificial_environment_data: + name: mimarks_s_miscellaneous_natural_or_artificial_environment_data + description: Data that complies with MimarksS combined with MiscellaneousNaturalOrArtificialEnvironment + title: MimarksSMiscellaneousNaturalOrArtificialEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - drug - - use - string_serialization: '{text};{integer}/[year|month|week|day|hour]' - slot_uri: MIXS:0000894 + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_miscellaneous_natural_or_artificial_environment_data multivalued: true - required: false - recommended: false - efficiency_percent: - name: efficiency_percent - annotations: - Preferred_unit: - tag: Preferred_unit - value: micromole per liter - description: Percentage of volatile solids removed from the anaerobic digestor - title: efficiency percent + range: MimarksSMiscellaneousNaturalOrArtificialEnvironment + inlined: true + inlined_as_list: true + mimarks_s_plant_associated_data: + name: mimarks_s_plant_associated_data + description: Data that complies with MimarksS combined with PlantAssociated + title: MimarksSPlantAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - percent - slot_uri: MIXS:0000657 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - elev: - name: elev - annotations: - Preferred_unit: - tag: Preferred_unit - value: meter - description: Elevation of the sampling site is its height above a fixed reference - point, most commonly the mean sea level. Elevation is mainly used when referring - to points on the earth's surface, while altitude is used for points above the - surface, such as an aircraft in flight or a spacecraft in orbit - title: elevation - examples: - - value: 100 meter - in_subset: - - environment + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_plant_associated_data + multivalued: true + range: MimarksSPlantAssociated + inlined: true + inlined_as_list: true + mimarks_s_sediment_data: + name: mimarks_s_sediment_data + description: Data that complies with MimarksS combined with Sediment + title: MimarksSSediment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - elevation - slot_uri: MIXS:0000093 - multivalued: false - range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - elevator: - name: elevator - description: The number of elevators within the built structure - title: elevator count - examples: - - value: '2' + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_sediment_data + multivalued: true + range: MimarksSSediment + inlined: true + inlined_as_list: true + mimarks_s_soil_data: + name: mimarks_s_soil_data + description: Data that complies with MimarksS combined with Soil + title: MimarksSSoil data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - count - slot_uri: MIXS:0000799 - multivalued: false - range: integer - required: false - recommended: false - emulsions: - name: emulsions - annotations: - Expected_value: - tag: Expected_value - value: emulsion name;measurement value - Preferred_unit: - tag: Preferred_unit - value: gram per liter - description: Amount or concentration of substances such as paints, adhesives, - mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion - types - title: emulsions + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_soil_data + multivalued: true + range: MimarksSSoil + inlined: true + inlined_as_list: true + mimarks_s_symbiont_associated_data: + name: mimarks_s_symbiont_associated_data + description: Data that complies with MimarksS combined with SymbiontAssociated + title: MimarksSSymbiontAssociated data from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000660 + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_symbiont_associated_data multivalued: true - required: false - recommended: false - encoded_traits: - name: encoded_traits - annotations: - Expected_value: - tag: Expected_value - value: 'for plasmid: antibiotic resistance; for phage: converting genes' - description: Should include key traits like antibiotic resistance or xenobiotic - degradation phenotypes for plasmids, converting genes for phage - title: encoded traits - examples: - - value: beta-lactamase class A - in_subset: - - nucleic acid sequence source + range: MimarksSSymbiontAssociated + inlined: true + inlined_as_list: true + mimarks_s_wastewater_sludge_data: + name: mimarks_s_wastewater_sludge_data + description: Data that complies with MimarksS combined with WastewaterSludge + title: MimarksSWastewaterSludge data from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text}' - slot_uri: MIXS:0000034 - multivalued: false - enrichment_protocol: - name: enrichment_protocol - description: The microbiological workflow or protocol followed to test for the - presence or enumeration of the target microbial analyte(s). Please provide a - PubMed or DOI reference for published protocols - title: enrichment protocol - examples: - - value: 'BAM Chapter 4: Enumeration of Escherichia coli and the Coliform Bacteria' + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_wastewater_sludge_data + multivalued: true + range: MimarksSWastewaterSludge + inlined: true + inlined_as_list: true + mimarks_s_water_data: + name: mimarks_s_water_data + description: Data that complies with MimarksS combined with Water + title: MimarksSWater data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - enrichment - - protocol - slot_uri: MIXS:0001177 - multivalued: false - range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}|{text}$ - interpolated: true - partial_match: true - env_broad_scale: - name: env_broad_scale - description: 'Report the major environmental system the sample or specimen came - from. The system(s) identified should have a coarse spatial grain, to provide - the general environmental context of where the sampling was done (e.g. in the - desert or a rainforest). We recommend using subclasses of EnvO s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. - EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS' - title: broad-scale environmental context - examples: - - value: rangeland biome [ENVO:01000247] - in_subset: - - environment + domain: MixsCompliantData + slot_uri: MIXS:mimarks_s_water_data + multivalued: true + range: MimarksSWater + inlined: true + inlined_as_list: true + mims_data: + name: mims_data + description: Data that complies with checklist Mims + title: Mims data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - context - - environmental - slot_uri: MIXS:0000012 - multivalued: false - range: string - required: true - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ - structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ - interpolated: true - partial_match: true - env_local_scale: - name: env_local_scale - annotations: - Expected_value: - tag: Expected_value - value: Environmental entities having causal influences upon the entity at - time of sampling - description: 'Report the entity or entities which are in the sample or specimen - s local vicinity and which you believe have significant causal influences on - your sample or specimen. We recommend using EnvO terms which are of smaller - spatial grain than your entry for env_broad_scale. Terms, such as anatomical - sites, from other OBO Library ontologies which interoperate with EnvO (e.g. - UBERON) are accepted in this field. EnvO documentation about how to use the - field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS' - title: local environmental context - examples: - - value: hillside [ENVO:01000333] - in_subset: - - environment - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - context - - environmental - string_serialization: '{termLabel} [{termID}]' - slot_uri: MIXS:0000013 - multivalued: false - required: true - env_medium: - name: env_medium - description: 'Report the environmental material(s) immediately surrounding the - sample or specimen at the time of sampling. We recommend using subclasses of - ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO - documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS - . Terms from other OBO ontologies are permissible as long as they reference - mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities - (e.g. a tree, a leaf, a table top)' - title: environmental medium - examples: - - value: bluegrass field soil [ENVO:00005789] - in_subset: - - environment - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - environmental - slot_uri: MIXS:0000014 - multivalued: false - range: string - required: true - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ - structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ - interpolated: true - partial_match: true - env_monitoring_zone: - name: env_monitoring_zone - annotations: - Expected_value: - tag: Expected_value - value: ENVO - description: An environmental monitoring zone is a formal designation as part - of an environmental monitoring program, in which areas of a food production - facility are categorized, commonly as zones 1-4, based on likelihood or risk - of foodborne pathogen contamination. This field accepts terms listed under food - production environmental monitoring zone (http://purl.obolibrary.org/obo/ENVO). - Please add a term to indicate the environmental monitoring zone the sample was - taken from - title: food production environmental monitoring zone - examples: - - value: Zone 1 + domain: MixsCompliantData + slot_uri: MIXS:mims_data + multivalued: true + range: Mims + inlined: true + inlined_as_list: true + mims_agriculture_data: + name: mims_agriculture_data + description: Data that complies with Mims combined with Agriculture + title: MimsAgriculture data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - environmental - - food - - production - string_serialization: '{text}' - slot_uri: MIXS:0001254 - multivalued: false - required: false - recommended: false - escalator: - name: escalator - description: The number of escalators within the built structure - title: escalator count - examples: - - value: '4' + domain: MixsCompliantData + slot_uri: MIXS:mims_agriculture_data + multivalued: true + range: MimsAgriculture + inlined: true + inlined_as_list: true + mims_air_data: + name: mims_air_data + description: Data that complies with Mims combined with Air + title: MimsAir data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - count - slot_uri: MIXS:0000800 - multivalued: false - range: integer - required: false - recommended: false - estimated_size: - name: estimated_size - annotations: - Expected_value: - tag: Expected_value - value: number of base pairs - description: The estimated size of the genome prior to sequencing. Of particular - importance in the sequencing of (eukaryotic) genome which could remain in draft - form for a long or unspecified period - title: estimated size - examples: - - value: 300000 bp - in_subset: - - nucleic acid sequence source + domain: MixsCompliantData + slot_uri: MIXS:mims_air_data + multivalued: true + range: MimsAir + inlined: true + inlined_as_list: true + mims_built_environment_data: + name: mims_built_environment_data + description: Data that complies with Mims combined with BuiltEnvironment + title: MimsBuiltEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - size - string_serialization: '{integer} bp' - slot_uri: MIXS:0000024 - multivalued: false - ethnicity: - name: ethnicity - annotations: - Expected_value: - tag: Expected_value - value: text recommend from Wikipedia list - description: A category of people who identify with each other, usually on the - basis of presumed similarities such as a common language, ancestry, history, - society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups - title: ethnicity - examples: - - value: native american + domain: MixsCompliantData + slot_uri: MIXS:mims_built_environment_data + multivalued: true + range: MimsBuiltEnvironment + inlined: true + inlined_as_list: true + mims_food_animal_and_animal_feed_data: + name: mims_food_animal_and_animal_feed_data + description: Data that complies with Mims combined with FoodAnimalAndAnimalFeed + title: MimsFoodAnimalAndAnimalFeed data from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text}' - slot_uri: MIXS:0000895 + domain: MixsCompliantData + slot_uri: MIXS:mims_food_animal_and_animal_feed_data multivalued: true - required: false - recommended: false - ethylbenzene: - name: ethylbenzene - annotations: - Preferred_unit: - tag: Preferred_unit - value: milligram per liter, parts per million - description: Concentration of ethylbenzene in the sample - title: ethylbenzene + range: MimsFoodAnimalAndAnimalFeed + inlined: true + inlined_as_list: true + mims_food_farm_environment_data: + name: mims_food_farm_environment_data + description: Data that complies with Mims combined with FoodFarmEnvironment + title: MimsFoodFarmEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000155 - multivalued: false - range: string - recommended: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - exp_duct: - name: exp_duct - annotations: - Preferred_unit: - tag: Preferred_unit - value: square meter - description: The amount of exposed ductwork in the room - title: exposed ductwork + domain: MixsCompliantData + slot_uri: MIXS:mims_food_farm_environment_data + multivalued: true + range: MimsFoodFarmEnvironment + inlined: true + inlined_as_list: true + mims_food_food_production_facility_data: + name: mims_food_food_production_facility_data + description: Data that complies with Mims combined with FoodFoodProductionFacility + title: MimsFoodFoodProductionFacility data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000144 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - exp_pipe: - name: exp_pipe - description: The number of exposed pipes in the room - title: exposed pipes + domain: MixsCompliantData + slot_uri: MIXS:mims_food_food_production_facility_data + multivalued: true + range: MimsFoodFoodProductionFacility + inlined: true + inlined_as_list: true + mims_food_human_foods_data: + name: mims_food_human_foods_data + description: Data that complies with Mims combined with FoodHumanFoods + title: MimsFoodHumanFoods data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - pipes - slot_uri: MIXS:0000220 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{integer} {text}$ - interpolated: true - partial_match: true - experimental_factor: - name: experimental_factor - annotations: - Expected_value: - tag: Expected_value - value: text or EFO and/or OBI - description: Variable aspects of an experiment design that can be used to describe - an experiment, or set of experiments, in an increasingly detailed manner. This - field accepts ontology terms from Experimental Factor Ontology (EFO) and/or - Ontology for Biomedical Investigations (OBI) - title: experimental factor - examples: - - value: time series design [EFO:0001779] - in_subset: - - investigation + domain: MixsCompliantData + slot_uri: MIXS:mims_food_human_foods_data + multivalued: true + range: MimsFoodHumanFoods + inlined: true + inlined_as_list: true + mims_host_associated_data: + name: mims_host_associated_data + description: Data that complies with Mims combined with HostAssociated + title: MimsHostAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - experimental - - factor - string_serialization: '{termLabel} [{termID}]|{text}' - slot_uri: MIXS:0000008 + domain: MixsCompliantData + slot_uri: MIXS:mims_host_associated_data multivalued: true - range: string - pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ - ext_door: - name: ext_door - description: The number of exterior doors in the built structure - title: exterior door count + range: MimsHostAssociated + inlined: true + inlined_as_list: true + mims_human_associated_data: + name: mims_human_associated_data + description: Data that complies with Mims combined with HumanAssociated + title: MimsHumanAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - count - - door - - exterior - slot_uri: MIXS:0000170 - multivalued: false - range: integer - required: false - recommended: false - ext_wall_orient: - name: ext_wall_orient - description: The orientation of the exterior wall - title: orientations of exterior wall - examples: - - value: northwest + domain: MixsCompliantData + slot_uri: MIXS:mims_human_associated_data + multivalued: true + range: MimsHumanAssociated + inlined: true + inlined_as_list: true + mims_human_gut_data: + name: mims_human_gut_data + description: Data that complies with Mims combined with HumanGut + title: MimsHumanGut data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - exterior - - wall - slot_uri: MIXS:0000817 - multivalued: false - range: SHARED_ENUM_0 - required: false - recommended: false - ext_window_orient: - name: ext_window_orient - description: The compass direction the exterior window of the room is facing - title: orientations of exterior window - examples: - - value: southwest + domain: MixsCompliantData + slot_uri: MIXS:mims_human_gut_data + multivalued: true + range: MimsHumanGut + inlined: true + inlined_as_list: true + mims_human_oral_data: + name: mims_human_oral_data + description: Data that complies with Mims combined with HumanOral + title: MimsHumanOral data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - exterior - - window - slot_uri: MIXS:0000818 - multivalued: false - range: SHARED_ENUM_0 - required: false - recommended: false - extr_weather_event: - name: extr_weather_event - description: Unusual weather events that may have affected microbial populations. - Multiple terms can be separated by pipes, listed in reverse chronological order - title: extreme weather event - examples: - - value: hail + domain: MixsCompliantData + slot_uri: MIXS:mims_human_oral_data + multivalued: true + range: MimsHumanOral + inlined: true + inlined_as_list: true + mims_human_skin_data: + name: mims_human_skin_data + description: Data that complies with Mims combined with HumanSkin + title: MimsHumanSkin data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - event - - extreme - - weather - slot_uri: MIXS:0001141 + domain: MixsCompliantData + slot_uri: MIXS:mims_human_skin_data multivalued: true - range: EXTR_WEATHER_EVENT_ENUM - required: false - recommended: false - extrachrom_elements: - name: extrachrom_elements - description: Do plasmids exist of significant phenotypic consequence (e.g. ones - that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids - (borrelia has 15+ plasmids) - title: extrachromosomal elements - examples: - - value: '5' - in_subset: - - nucleic acid sequence source + range: MimsHumanSkin + inlined: true + inlined_as_list: true + mims_human_vaginal_data: + name: mims_human_vaginal_data + description: Data that complies with Mims combined with HumanVaginal + title: MimsHumanVaginal data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000023 - multivalued: false - range: integer - extreme_event: - name: extreme_event - description: Unusual physical events that may have affected microbial populations - title: history/extreme events + domain: MixsCompliantData + slot_uri: MIXS:mims_human_vaginal_data + multivalued: true + range: MimsHumanVaginal + inlined: true + inlined_as_list: true + mims_hydrocarbon_resources_cores_data: + name: mims_hydrocarbon_resources_cores_data + description: Data that complies with Mims combined with HydrocarbonResourcesCores + title: MimsHydrocarbonResourcesCores data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - event - - history - slot_uri: MIXS:0000320 - multivalued: false - range: datetime - facility_type: - name: facility_type - description: Establishment details about the type of facility where the sample - was taken. This is independent of the specific product(s) within the facility - title: facility type - examples: - - value: manufacturing-processing + domain: MixsCompliantData + slot_uri: MIXS:mims_hydrocarbon_resources_cores_data + multivalued: true + range: MimsHydrocarbonResourcesCores + inlined: true + inlined_as_list: true + mims_hydrocarbon_resources_fluids_swabs_data: + name: mims_hydrocarbon_resources_fluids_swabs_data + description: Data that complies with Mims combined with HydrocarbonResourcesFluidsSwabs + title: MimsHydrocarbonResourcesFluidsSwabs data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - facility - - type - slot_uri: MIXS:0001252 + domain: MixsCompliantData + slot_uri: MIXS:mims_hydrocarbon_resources_fluids_swabs_data multivalued: true - range: FACILITY_TYPE_ENUM - required: false - recommended: false - fao_class: - name: fao_class - description: Soil classification from the FAO World Reference Database for Soil - Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups - title: soil_taxonomic/FAO classification - examples: - - value: Luvisols + range: MimsHydrocarbonResourcesFluidsSwabs + inlined: true + inlined_as_list: true + mims_microbial_mat_biofilm_data: + name: mims_microbial_mat_biofilm_data + description: Data that complies with Mims combined with MicrobialMatBiofilm + title: MimsMicrobialMatBiofilm data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - classification - slot_uri: MIXS:0001083 - multivalued: false - range: FAO_CLASS_ENUM - farm_equip: - name: farm_equip - description: List of equipment used for planting, fertilization, harvesting, irrigation, - land levelling, residue management, weeding or transplanting during the growing - season. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). - Multiple terms can be separated by pipes - title: farm equipment used - examples: - - value: combine harvester [AGRO:00000473] + domain: MixsCompliantData + slot_uri: MIXS:mims_microbial_mat_biofilm_data + multivalued: true + range: MimsMicrobialMatBiofilm + inlined: true + inlined_as_list: true + mims_miscellaneous_natural_or_artificial_environment_data: + name: mims_miscellaneous_natural_or_artificial_environment_data + description: Data that complies with Mims combined with MiscellaneousNaturalOrArtificialEnvironment + title: MimsMiscellaneousNaturalOrArtificialEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - equipment - - farm - - use - slot_uri: MIXS:0001126 + domain: MixsCompliantData + slot_uri: MIXS:mims_miscellaneous_natural_or_artificial_environment_data multivalued: true - range: string - required: false - recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ - structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ - interpolated: true - partial_match: true - farm_equip_san: - name: farm_equip_san - annotations: - Expected_value: - tag: Expected_value - value: text or commercial name of sanitizer or class of sanitizer or active - ingredient in sanitizer - Preferred_unit: - tag: Preferred_unit - value: parts per million - description: Method used to sanitize growing and harvesting equipment. This can - including type and concentration of sanitizing solution. Multiple terms can - be separated by one or more pipes - title: farm equipment sanitization - examples: - - value: hot water pressure wash, hypochlorite solution, 50 parts per million + range: MimsMiscellaneousNaturalOrArtificialEnvironment + inlined: true + inlined_as_list: true + mims_plant_associated_data: + name: mims_plant_associated_data + description: Data that complies with Mims combined with PlantAssociated + title: MimsPlantAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - equipment - - farm - string_serialization: '{text} {float} {unit}' - slot_uri: MIXS:0001124 + domain: MixsCompliantData + slot_uri: MIXS:mims_plant_associated_data multivalued: true - required: false - recommended: false - farm_equip_san_freq: - name: farm_equip_san_freq - description: The number of times farm equipment is cleaned. Frequency of cleaning - might be on a Daily basis, Weekly, Monthly, Quarterly or Annually - title: farm equipment sanitization frequency - examples: - - value: Biweekly + range: MimsPlantAssociated + inlined: true + inlined_as_list: true + mims_sediment_data: + name: mims_sediment_data + description: Data that complies with Mims combined with Sediment + title: MimsSediment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - equipment - - farm - - frequency - slot_uri: MIXS:0001125 - multivalued: false - range: string - required: false - recommended: false - farm_equip_shared: - name: farm_equip_shared - description: List of planting, growing or harvesting equipment shared with other - farms. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). - Multiple terms can be separated by pipes - title: equipment shared with other farms - examples: - - value: combine harvester [AGRO:00000473] + domain: MixsCompliantData + slot_uri: MIXS:mims_sediment_data + multivalued: true + range: MimsSediment + inlined: true + inlined_as_list: true + mims_soil_data: + name: mims_soil_data + description: Data that complies with Mims combined with Soil + title: MimsSoil data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - equipment - - farm - slot_uri: MIXS:0001123 + domain: MixsCompliantData + slot_uri: MIXS:mims_soil_data multivalued: true - range: string - required: false - recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ - structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ - interpolated: true - partial_match: true - farm_water_source: - name: farm_water_source - description: Source of water used on the farm for irrigation of crops or watering - of livestock - title: farm watering water source - examples: - - value: well - description: was water well (ENVO:01000002) + range: MimsSoil + inlined: true + inlined_as_list: true + mims_symbiont_associated_data: + name: mims_symbiont_associated_data + description: Data that complies with Mims combined with SymbiontAssociated + title: MimsSymbiontAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - farm - - source - - water - slot_uri: MIXS:0001110 - range: FARM_WATER_SOURCE_ENUM - recommended: true - feat_pred: - name: feat_pred - description: Method used to predict UViGs features such as ORFs, integration site, - etc - title: feature prediction - examples: - - value: Prodigal;2.6.3;default parameters - in_subset: - - sequencing + domain: MixsCompliantData + slot_uri: MIXS:mims_symbiont_associated_data + multivalued: true + range: MimsSymbiontAssociated + inlined: true + inlined_as_list: true + mims_wastewater_sludge_data: + name: mims_wastewater_sludge_data + description: Data that complies with Mims combined with WastewaterSludge + title: MimsWastewaterSludge data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - feature - - predict - slot_uri: MIXS:0000061 - multivalued: false - range: string - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{software};{version};{parameters}$ - interpolated: true - partial_match: true - ferm_chem_add: - name: ferm_chem_add - annotations: - Expected_value: - tag: Expected_value - value: chemical ingredient - description: Any chemicals that are added to the fermentation process to achieve - the desired final product - title: fermentation chemical additives - examples: - - value: salt + domain: MixsCompliantData + slot_uri: MIXS:mims_wastewater_sludge_data + multivalued: true + range: MimsWastewaterSludge + inlined: true + inlined_as_list: true + mims_water_data: + name: mims_water_data + description: Data that complies with Mims combined with Water + title: MimsWater data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - fermentation - string_serialization: '{float} {unit}' - slot_uri: MIXS:0001185 + domain: MixsCompliantData + slot_uri: MIXS:mims_water_data multivalued: true - recommended: true - ferm_chem_add_perc: - name: ferm_chem_add_perc - annotations: - Preferred_unit: - tag: Preferred_unit - value: percentage - description: The amount of chemical added to the fermentation process - title: fermentation chemical additives percentage - examples: - - value: '0.01' + range: MimsWater + inlined: true + inlined_as_list: true + misag_data: + name: misag_data + description: Data that complies with checklist Misag + title: Misag data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - fermentation - - percent - slot_uri: MIXS:0001186 + domain: MixsCompliantData + slot_uri: MIXS:misag_data multivalued: true - range: float - recommended: true - ferm_headspace_oxy: - name: ferm_headspace_oxy - annotations: - Preferred_unit: - tag: Preferred_unit - value: percentage - description: The amount of headspace oxygen in a fermentation vessel - title: fermentation headspace oxygen - examples: - - value: '0.05' + range: Misag + inlined: true + inlined_as_list: true + misag_agriculture_data: + name: misag_agriculture_data + description: Data that complies with Misag combined with Agriculture + title: MisagAgriculture data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - fermentation - - oxygen - slot_uri: MIXS:0001187 - multivalued: false - range: float - recommended: true - ferm_medium: - name: ferm_medium - description: The growth medium used for the fermented food fermentation process, - which supplies the required nutrients. Usually this includes a carbon and nitrogen - source, water, micronutrients and chemical additives - title: fermentation medium - examples: - - value: molasses + domain: MixsCompliantData + slot_uri: MIXS:misag_agriculture_data + multivalued: true + range: MisagAgriculture + inlined: true + inlined_as_list: true + misag_air_data: + name: misag_air_data + description: Data that complies with Misag combined with Air + title: MisagAir data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - fermentation - slot_uri: MIXS:0001188 - multivalued: false - range: string - recommended: true - ferm_pH: - name: ferm_pH - description: The pH of the fermented food fermentation process - title: fermentation pH - examples: - - value: '4.5' + domain: MixsCompliantData + slot_uri: MIXS:misag_air_data + multivalued: true + range: MisagAir + inlined: true + inlined_as_list: true + misag_built_environment_data: + name: misag_built_environment_data + description: Data that complies with Misag combined with BuiltEnvironment + title: MisagBuiltEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - fermentation - - ph - slot_uri: MIXS:0001189 - multivalued: false - range: float - recommended: true - ferm_rel_humidity: - name: ferm_rel_humidity - annotations: - Preferred_unit: - tag: Preferred_unit - value: percentage - description: The relative humidity of the fermented food fermentation process - title: fermentation relative humidity - comments: - - percent or float? - examples: - - value: 95% + domain: MixsCompliantData + slot_uri: MIXS:misag_built_environment_data + multivalued: true + range: MisagBuiltEnvironment + inlined: true + inlined_as_list: true + misag_food_animal_and_animal_feed_data: + name: misag_food_animal_and_animal_feed_data + description: Data that complies with Misag combined with FoodAnimalAndAnimalFeed + title: MisagFoodAnimalAndAnimalFeed data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - fermentation - - humidity - - relative - slot_uri: MIXS:0001190 - range: string - recommended: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - ferm_temp: - name: ferm_temp - annotations: - Preferred_unit: - tag: Preferred_unit - value: degree Celsius - description: The temperature of the fermented food fermentation process - title: fermentation temperature - examples: - - value: 22 degrees Celsius + domain: MixsCompliantData + slot_uri: MIXS:misag_food_animal_and_animal_feed_data + multivalued: true + range: MisagFoodAnimalAndAnimalFeed + inlined: true + inlined_as_list: true + misag_food_farm_environment_data: + name: misag_food_farm_environment_data + description: Data that complies with Misag combined with FoodFarmEnvironment + title: MisagFoodFarmEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - fermentation - - temperature - slot_uri: MIXS:0001191 - multivalued: false - range: string - recommended: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - ferm_time: - name: ferm_time - annotations: - Preferred_unit: - tag: Preferred_unit - value: days - description: The time duration of the fermented food fermentation process - title: fermentation time - examples: - - value: P10D + domain: MixsCompliantData + slot_uri: MIXS:misag_food_farm_environment_data + multivalued: true + range: MisagFoodFarmEnvironment + inlined: true + inlined_as_list: true + misag_food_food_production_facility_data: + name: misag_food_food_production_facility_data + description: Data that complies with Misag combined with FoodFoodProductionFacility + title: MisagFoodFoodProductionFacility data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - fermentation - - time - slot_uri: MIXS:0001192 - multivalued: false - range: string - recommended: true - pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ - structured_pattern: - syntax: ^{duration}$ - interpolated: true - partial_match: true - ferm_vessel: - name: ferm_vessel - description: The type of vessel used for containment of the fermentation - title: fermentation vessel - examples: - - value: steel drum + domain: MixsCompliantData + slot_uri: MIXS:misag_food_food_production_facility_data + multivalued: true + range: MisagFoodFoodProductionFacility + inlined: true + inlined_as_list: true + misag_food_human_foods_data: + name: misag_food_human_foods_data + description: Data that complies with Misag combined with FoodHumanFoods + title: MisagFoodHumanFoods data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - fermentation - slot_uri: MIXS:0001193 - multivalued: false - range: string - recommended: true - fertilizer_admin: - name: fertilizer_admin - description: Type of fertilizer or amendment added to the soil or water for the - purpose of improving substrate health and quality for plant growth. This field - accepts terms listed under agronomic fertilizer (http://purl.obolibrary.org/obo/AGRO_00002062). - Multiple terms may apply and can be separated by pipes, listing in reverse chronological - order - title: fertilizer administration - examples: - - value: fish emulsion [AGRO:00000082] + domain: MixsCompliantData + slot_uri: MIXS:misag_food_human_foods_data + multivalued: true + range: MisagFoodHumanFoods + inlined: true + inlined_as_list: true + misag_host_associated_data: + name: misag_host_associated_data + description: Data that complies with Misag combined with HostAssociated + title: MisagHostAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - administration - slot_uri: MIXS:0001127 - multivalued: false - range: string - required: false - recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ - structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ - interpolated: true - partial_match: true - fertilizer_date: - name: fertilizer_date - description: Date of administration of soil amendment or fertilizer. Multiple - terms may apply and can be separated by pipes, listing in reverse chronological - order - title: fertilizer administration date - examples: - - value: '2018-05-11T10:00:00+01:00' + domain: MixsCompliantData + slot_uri: MIXS:misag_host_associated_data + multivalued: true + range: MisagHostAssociated + inlined: true + inlined_as_list: true + misag_human_associated_data: + name: misag_human_associated_data + description: Data that complies with Misag combined with HumanAssociated + title: MisagHumanAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - administration - - date - slot_uri: MIXS:0001128 - multivalued: false - range: datetime - required: false - recommended: false - fertilizer_regm: - name: fertilizer_regm - annotations: - Expected_value: - tag: Expected_value - value: fertilizer name;fertilizer amount;treatment interval and duration - Preferred_unit: - tag: Preferred_unit - value: gram, mole per liter, milligram per liter - description: Information about treatment involving the use of fertilizers; should - include the name of fertilizer, amount administered, treatment regimen including - how many times the treatment was repeated, how long each treatment lasted, and - the start and end time of the entire treatment; can include multiple fertilizer - regimens - title: fertilizer regimen - examples: - - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M + domain: MixsCompliantData + slot_uri: MIXS:misag_human_associated_data + multivalued: true + range: MisagHumanAssociated + inlined: true + inlined_as_list: true + misag_human_gut_data: + name: misag_human_gut_data + description: Data that complies with Misag combined with HumanGut + title: MisagHumanGut data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - regimen - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000556 + domain: MixsCompliantData + slot_uri: MIXS:misag_human_gut_data multivalued: true - required: false - recommended: false - field: - name: field - description: Name of the hydrocarbon field (e.g. Albacora) - title: field name + range: MisagHumanGut + inlined: true + inlined_as_list: true + misag_human_oral_data: + name: misag_human_oral_data + description: Data that complies with Misag combined with HumanOral + title: MisagHumanOral data from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000291 - multivalued: false - range: string - recommended: true - filter_type: - name: filter_type - description: A device which removes solid particulates or airborne molecular contaminants - title: filter type - examples: - - value: HEPA + domain: MixsCompliantData + slot_uri: MIXS:misag_human_oral_data + multivalued: true + range: MisagHumanOral + inlined: true + inlined_as_list: true + misag_human_skin_data: + name: misag_human_skin_data + description: Data that complies with Misag combined with HumanSkin + title: MisagHumanSkin data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - filter - - type - slot_uri: MIXS:0000765 + domain: MixsCompliantData + slot_uri: MIXS:misag_human_skin_data multivalued: true - range: FILTER_TYPE_ENUM - required: true - fire: - name: fire - description: Historical and/or physical evidence of fire - title: history/fire + range: MisagHumanSkin + inlined: true + inlined_as_list: true + misag_human_vaginal_data: + name: misag_human_vaginal_data + description: Data that complies with Misag combined with HumanVaginal + title: MisagHumanVaginal data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - history - slot_uri: MIXS:0001086 - multivalued: false - range: datetime - fireplace_type: - name: fireplace_type - description: A firebox with chimney - title: fireplace type - examples: - - value: wood burning + domain: MixsCompliantData + slot_uri: MIXS:misag_human_vaginal_data + multivalued: true + range: MisagHumanVaginal + inlined: true + inlined_as_list: true + misag_hydrocarbon_resources_cores_data: + name: misag_hydrocarbon_resources_cores_data + description: Data that complies with Misag combined with HydrocarbonResourcesCores + title: MisagHydrocarbonResourcesCores data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - type - slot_uri: MIXS:0000802 - multivalued: false - range: FIREPLACE_TYPE_ENUM - required: false - recommended: false - flooding: - name: flooding - description: Historical and/or physical evidence of flooding - title: history/flooding + domain: MixsCompliantData + slot_uri: MIXS:misag_hydrocarbon_resources_cores_data + multivalued: true + range: MisagHydrocarbonResourcesCores + inlined: true + inlined_as_list: true + misag_hydrocarbon_resources_fluids_swabs_data: + name: misag_hydrocarbon_resources_fluids_swabs_data + description: Data that complies with Misag combined with HydrocarbonResourcesFluidsSwabs + title: MisagHydrocarbonResourcesFluidsSwabs data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - history - slot_uri: MIXS:0000319 - multivalued: false - range: datetime - floor_age: - name: floor_age - annotations: - Preferred_unit: - tag: Preferred_unit - value: years, weeks, days - description: The time period since installment of the carpet or flooring - title: floor age + domain: MixsCompliantData + slot_uri: MIXS:misag_hydrocarbon_resources_fluids_swabs_data + multivalued: true + range: MisagHydrocarbonResourcesFluidsSwabs + inlined: true + inlined_as_list: true + misag_microbial_mat_biofilm_data: + name: misag_microbial_mat_biofilm_data + description: Data that complies with Misag combined with MicrobialMatBiofilm + title: MisagMicrobialMatBiofilm data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - age - - floor - slot_uri: MIXS:0000164 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - floor_area: - name: floor_area - annotations: - Preferred_unit: - tag: Preferred_unit - value: square meter - description: The area of the floor space within the room - title: floor area + domain: MixsCompliantData + slot_uri: MIXS:misag_microbial_mat_biofilm_data + multivalued: true + range: MisagMicrobialMatBiofilm + inlined: true + inlined_as_list: true + misag_miscellaneous_natural_or_artificial_environment_data: + name: misag_miscellaneous_natural_or_artificial_environment_data + description: Data that complies with Misag combined with MiscellaneousNaturalOrArtificialEnvironment + title: MisagMiscellaneousNaturalOrArtificialEnvironment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - area - - floor - slot_uri: MIXS:0000165 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - floor_cond: - name: floor_cond - description: The physical condition of the floor at the time of sampling; photos - or video preferred; use drawings to indicate location of damaged areas - title: floor condition - examples: - - value: new + domain: MixsCompliantData + slot_uri: MIXS:misag_miscellaneous_natural_or_artificial_environment_data + multivalued: true + range: MisagMiscellaneousNaturalOrArtificialEnvironment + inlined: true + inlined_as_list: true + misag_plant_associated_data: + name: misag_plant_associated_data + description: Data that complies with Misag combined with PlantAssociated + title: MisagPlantAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - condition - - floor - slot_uri: MIXS:0000803 - multivalued: false - range: SHARED_ENUM_3 - required: false - recommended: false - floor_count: - name: floor_count - description: The number of floors in the building, including basements and mechanical - penthouse - title: floor count + domain: MixsCompliantData + slot_uri: MIXS:misag_plant_associated_data + multivalued: true + range: MisagPlantAssociated + inlined: true + inlined_as_list: true + misag_sediment_data: + name: misag_sediment_data + description: Data that complies with Misag combined with Sediment + title: MisagSediment data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - count - - floor - slot_uri: MIXS:0000225 - multivalued: false - range: integer - required: false - recommended: false - floor_finish_mat: - name: floor_finish_mat - annotations: - Expected_value: - tag: Expected_value - value: enumeration - description: The floor covering type; the finished surface that is walked on - title: floor finish material - examples: - - value: carpet + domain: MixsCompliantData + slot_uri: MIXS:misag_sediment_data + multivalued: true + range: MisagSediment + inlined: true + inlined_as_list: true + misag_soil_data: + name: misag_soil_data + description: Data that complies with Misag combined with Soil + title: MisagSoil data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - floor - - material - string_serialization: '[tile|wood strip or parquet|carpet|rug|laminate wood|lineoleum|vinyl - composition tile|sheet vinyl|stone|bamboo|cork|terrazo|concrete|none;specify - unfinished|sealed|clear finish|paint]' - slot_uri: MIXS:0000804 - multivalued: false - required: false - recommended: false - floor_struc: - name: floor_struc - description: Refers to the structural elements and subfloor upon which the finish - flooring is installed - title: floor structure - examples: - - value: concrete + domain: MixsCompliantData + slot_uri: MIXS:misag_soil_data + multivalued: true + range: MisagSoil + inlined: true + inlined_as_list: true + misag_symbiont_associated_data: + name: misag_symbiont_associated_data + description: Data that complies with Misag combined with SymbiontAssociated + title: MisagSymbiontAssociated data from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - floor - slot_uri: MIXS:0000806 - multivalued: false - range: FLOOR_STRUC_ENUM - required: false - recommended: false - floor_thermal_mass: - name: floor_thermal_mass - annotations: - Preferred_unit: - tag: Preferred_unit - value: joule per degree Celsius - description: The ability of the floor to provide inertia against temperature fluctuations - title: floor thermal mass + domain: MixsCompliantData + slot_uri: MIXS:misag_symbiont_associated_data + multivalued: true + range: MisagSymbiontAssociated + inlined: true + inlined_as_list: true + misag_wastewater_sludge_data: + name: misag_wastewater_sludge_data + description: Data that complies with Misag combined with WastewaterSludge + title: MisagWastewaterSludge data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:misag_wastewater_sludge_data + multivalued: true + range: MisagWastewaterSludge + inlined: true + inlined_as_list: true + misag_water_data: + name: misag_water_data + description: Data that complies with Misag combined with Water + title: MisagWater data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:misag_water_data + multivalued: true + range: MisagWater + inlined: true + inlined_as_list: true + miuvig_data: + name: miuvig_data + description: Data that complies with checklist Miuvig + title: Miuvig data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_data + multivalued: true + range: Miuvig + inlined: true + inlined_as_list: true + miuvig_agriculture_data: + name: miuvig_agriculture_data + description: Data that complies with Miuvig combined with Agriculture + title: MiuvigAgriculture data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_agriculture_data + multivalued: true + range: MiuvigAgriculture + inlined: true + inlined_as_list: true + miuvig_air_data: + name: miuvig_air_data + description: Data that complies with Miuvig combined with Air + title: MiuvigAir data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_air_data + multivalued: true + range: MiuvigAir + inlined: true + inlined_as_list: true + miuvig_built_environment_data: + name: miuvig_built_environment_data + description: Data that complies with Miuvig combined with BuiltEnvironment + title: MiuvigBuiltEnvironment data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_built_environment_data + multivalued: true + range: MiuvigBuiltEnvironment + inlined: true + inlined_as_list: true + miuvig_food_animal_and_animal_feed_data: + name: miuvig_food_animal_and_animal_feed_data + description: Data that complies with Miuvig combined with FoodAnimalAndAnimalFeed + title: MiuvigFoodAnimalAndAnimalFeed data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_food_animal_and_animal_feed_data + multivalued: true + range: MiuvigFoodAnimalAndAnimalFeed + inlined: true + inlined_as_list: true + miuvig_food_farm_environment_data: + name: miuvig_food_farm_environment_data + description: Data that complies with Miuvig combined with FoodFarmEnvironment + title: MiuvigFoodFarmEnvironment data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_food_farm_environment_data + multivalued: true + range: MiuvigFoodFarmEnvironment + inlined: true + inlined_as_list: true + miuvig_food_food_production_facility_data: + name: miuvig_food_food_production_facility_data + description: Data that complies with Miuvig combined with FoodFoodProductionFacility + title: MiuvigFoodFoodProductionFacility data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_food_food_production_facility_data + multivalued: true + range: MiuvigFoodFoodProductionFacility + inlined: true + inlined_as_list: true + miuvig_food_human_foods_data: + name: miuvig_food_human_foods_data + description: Data that complies with Miuvig combined with FoodHumanFoods + title: MiuvigFoodHumanFoods data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_food_human_foods_data + multivalued: true + range: MiuvigFoodHumanFoods + inlined: true + inlined_as_list: true + miuvig_host_associated_data: + name: miuvig_host_associated_data + description: Data that complies with Miuvig combined with HostAssociated + title: MiuvigHostAssociated data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_host_associated_data + multivalued: true + range: MiuvigHostAssociated + inlined: true + inlined_as_list: true + miuvig_human_associated_data: + name: miuvig_human_associated_data + description: Data that complies with Miuvig combined with HumanAssociated + title: MiuvigHumanAssociated data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_human_associated_data + multivalued: true + range: MiuvigHumanAssociated + inlined: true + inlined_as_list: true + miuvig_human_gut_data: + name: miuvig_human_gut_data + description: Data that complies with Miuvig combined with HumanGut + title: MiuvigHumanGut data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_human_gut_data + multivalued: true + range: MiuvigHumanGut + inlined: true + inlined_as_list: true + miuvig_human_oral_data: + name: miuvig_human_oral_data + description: Data that complies with Miuvig combined with HumanOral + title: MiuvigHumanOral data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_human_oral_data + multivalued: true + range: MiuvigHumanOral + inlined: true + inlined_as_list: true + miuvig_human_skin_data: + name: miuvig_human_skin_data + description: Data that complies with Miuvig combined with HumanSkin + title: MiuvigHumanSkin data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_human_skin_data + multivalued: true + range: MiuvigHumanSkin + inlined: true + inlined_as_list: true + miuvig_human_vaginal_data: + name: miuvig_human_vaginal_data + description: Data that complies with Miuvig combined with HumanVaginal + title: MiuvigHumanVaginal data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_human_vaginal_data + multivalued: true + range: MiuvigHumanVaginal + inlined: true + inlined_as_list: true + miuvig_hydrocarbon_resources_cores_data: + name: miuvig_hydrocarbon_resources_cores_data + description: Data that complies with Miuvig combined with HydrocarbonResourcesCores + title: MiuvigHydrocarbonResourcesCores data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_hydrocarbon_resources_cores_data + multivalued: true + range: MiuvigHydrocarbonResourcesCores + inlined: true + inlined_as_list: true + miuvig_hydrocarbon_resources_fluids_swabs_data: + name: miuvig_hydrocarbon_resources_fluids_swabs_data + description: Data that complies with Miuvig combined with HydrocarbonResourcesFluidsSwabs + title: MiuvigHydrocarbonResourcesFluidsSwabs data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_hydrocarbon_resources_fluids_swabs_data + multivalued: true + range: MiuvigHydrocarbonResourcesFluidsSwabs + inlined: true + inlined_as_list: true + miuvig_microbial_mat_biofilm_data: + name: miuvig_microbial_mat_biofilm_data + description: Data that complies with Miuvig combined with MicrobialMatBiofilm + title: MiuvigMicrobialMatBiofilm data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_microbial_mat_biofilm_data + multivalued: true + range: MiuvigMicrobialMatBiofilm + inlined: true + inlined_as_list: true + miuvig_miscellaneous_natural_or_artificial_environment_data: + name: miuvig_miscellaneous_natural_or_artificial_environment_data + description: Data that complies with Miuvig combined with MiscellaneousNaturalOrArtificialEnvironment + title: MiuvigMiscellaneousNaturalOrArtificialEnvironment data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_miscellaneous_natural_or_artificial_environment_data + multivalued: true + range: MiuvigMiscellaneousNaturalOrArtificialEnvironment + inlined: true + inlined_as_list: true + miuvig_plant_associated_data: + name: miuvig_plant_associated_data + description: Data that complies with Miuvig combined with PlantAssociated + title: MiuvigPlantAssociated data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_plant_associated_data + multivalued: true + range: MiuvigPlantAssociated + inlined: true + inlined_as_list: true + miuvig_sediment_data: + name: miuvig_sediment_data + description: Data that complies with Miuvig combined with Sediment + title: MiuvigSediment data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_sediment_data + multivalued: true + range: MiuvigSediment + inlined: true + inlined_as_list: true + miuvig_soil_data: + name: miuvig_soil_data + description: Data that complies with Miuvig combined with Soil + title: MiuvigSoil data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_soil_data + multivalued: true + range: MiuvigSoil + inlined: true + inlined_as_list: true + miuvig_symbiont_associated_data: + name: miuvig_symbiont_associated_data + description: Data that complies with Miuvig combined with SymbiontAssociated + title: MiuvigSymbiontAssociated data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_symbiont_associated_data + multivalued: true + range: MiuvigSymbiontAssociated + inlined: true + inlined_as_list: true + miuvig_wastewater_sludge_data: + name: miuvig_wastewater_sludge_data + description: Data that complies with Miuvig combined with WastewaterSludge + title: MiuvigWastewaterSludge data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_wastewater_sludge_data + multivalued: true + range: MiuvigWastewaterSludge + inlined: true + inlined_as_list: true + miuvig_water_data: + name: miuvig_water_data + description: Data that complies with Miuvig combined with Water + title: MiuvigWater data + from_schema: https://w3id.org/mixs-6-2-rc + domain: MixsCompliantData + slot_uri: MIXS:miuvig_water_data + multivalued: true + range: MiuvigWater + inlined: true + inlined_as_list: true + HACCP_term: + name: HACCP_term + description: Hazard Analysis Critical Control Points (HACCP) food safety terms; + This field accepts terms listed under HACCP guide food safety term (http://purl.obolibrary.org/obo/FOODON_03530221) + title: Hazard Analysis Critical Control Points (HACCP) guide food safety term + examples: + - value: tetrodotoxic poisoning [FOODON:03530249] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - floor - - mass - slot_uri: MIXS:0000166 - multivalued: false + - food + - term + slot_uri: MIXS:0001215 + multivalued: true range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: ^{termLabel} \[{termID}\]$ interpolated: true partial_match: true - floor_water_mold: - name: floor_water_mold - description: Signs of the presence of mold or mildew in a room - title: floor signs of water/mold + IFSAC_category: + name: IFSAC_category + annotations: + Expected_value: + tag: Expected_value + value: IFSAC term + description: 'The IFSAC food categorization scheme has five distinct levels to + which foods can be assigned, depending upon the type of food. First, foods are + assigned to one of four food groups (aquatic animals, land animals, plants, + and other). Food groups include increasingly specific food categories; dairy, + eggs, meat and poultry, and game are in the land animal food group, and the + category meat and poultry is further subdivided into more specific categories + of meat (beef, pork, other meat) and poultry (chicken, turkey, other poultry). + Finally, foods are differentiated by differences in food processing (such as + pasteurized fluid dairy products, unpasteurized fluid dairy products, pasteurized + solid and semi-solid dairy products, and unpasteurized solid and semi-solid + dairy products. An IFSAC food category chart is available from https://www.cdc.gov/foodsafety/ifsac/projects/food-categorization-scheme.html + PMID: 28926300' + title: Interagency Food Safety Analytics Collaboration (IFSAC) category examples: - - value: ceiling discoloration + - value: Plants:Produce:Vegetables:Herbs:Dried Herbs from_schema: https://w3id.org/mixs-6-2-rc keywords: - - floor - slot_uri: MIXS:0000805 - multivalued: false - range: FLOOR_WATER_MOLD_ENUM - required: false - recommended: false - fluor: - name: fluor + - food + string_serialization: '{text}' + slot_uri: MIXS:0001179 + multivalued: true + required: true + abs_air_humidity: + name: abs_air_humidity annotations: Preferred_unit: tag: Preferred_unit - value: milligram chlorophyll a per cubic meter, volts - description: Raw or converted fluorescence of water - title: fluorescence + value: gram per gram, kilogram per kilogram, kilogram, pound + description: Actual mass of water vapor - mh20 - present in the air water vapor + mixture + title: absolute air humidity examples: - - value: 2.5 volts + - value: 9 gram per gram from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000704 + keywords: + - absolute + - air + - humidity + slot_uri: MIXS:0000122 multivalued: false range: string - required: false - recommended: false + required: true pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - foetal_health_stat: - name: foetal_health_stat - description: Specification of foetal health status, should also include abortion - title: amniotic fluid/foetal health status - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - status - slot_uri: MIXS:0000275 - multivalued: false - range: string - required: false - recommended: false - food_additive: - name: food_additive + adapters: + name: adapters annotations: Expected_value: tag: Expected_value - value: FOODON:03412972 - description: A substance or substances added to food to maintain or improve safety - and freshness, to improve or maintain nutritional value, or improve taste, texture - and appearance. This field accepts terms listed under food additive (http://purl.obolibrary.org/obo/FOODON_03412972). - Multiple terms can be separated by one or more pipes, but please consider limiting - this list to the top 5 ingredients listed in order as on the food label. See - also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors - title: food additive + value: adapter A and B sequence + description: Adapters provide priming sequences for both amplification and sequencing + of the sample-library fragments. Both adapters should be reported; in uppercase + letters + title: adapters examples: - - value: xanthan gum [FOODON:03413321] + - value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - food - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001200 - multivalued: true - required: false - recommended: false - food_allergen_label: - name: food_allergen_label + string_serialization: '{dna};{dna}' + slot_uri: MIXS:0000048 + multivalued: false + add_recov_method: + name: add_recov_method annotations: Expected_value: tag: Expected_value - value: FOODON:03510213 - description: A label indication that the product contains a recognized allergen. - This field accepts terms listed under dietary claim or use (http://purl.obolibrary.org/obo/FOODON_03510213) - title: food allergen labeling + value: enumeration;timestamp + description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed + for increase of hydrocarbon recovery from resource and start date for each one + of them. If "other" is specified, please propose entry in "additional info" + field + title: secondary and tertiary recovery methods and start date examples: - - value: food allergen labelling about crustaceans and products thereof [FOODON:03510215] + - value: Polymer Addition;2018-06-21T14:30Z from_schema: https://w3id.org/mixs-6-2-rc keywords: - - food - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001201 - multivalued: true - required: false - recommended: false - food_clean_proc: - name: food_clean_proc - description: The process of cleaning food to separate other environmental materials - from the food source. Multiple terms can be separated by pipes - title: food cleaning process - examples: - - value: rinsed with water - description: was rinsed with water|scrubbed with brush - - value: scrubbed with brush - description: was rinsed with water|scrubbed with brush + - date + - method + - recover + - secondary + - start + string_serialization: '[Water Injection|Dump Flood|Gas Injection|Wag Immiscible + Injection|Polymer Addition|Surfactant Addition|Not Applicable|other];{timestamp}' + slot_uri: MIXS:0001009 + multivalued: false + required: true + additional_info: + name: additional_info + description: Information that doesn't fit anywhere else. Can also be used to propose + new entries for fields with controlled vocabulary + title: additional info from_schema: https://w3id.org/mixs-6-2-rc keywords: - - food - - process - slot_uri: MIXS:0001182 - range: FOOD_CLEAN_PROC_ENUM + - information + slot_uri: MIXS:0000300 + multivalued: false + range: string required: false recommended: false - food_contact_surf: - name: food_contact_surf + address: + name: address annotations: Expected_value: tag: Expected_value - value: FOODON:03500010 - description: The specific container or coating materials in direct contact with - the food. Multiple values can be assigned. This field accepts terms listed - under food contact surface (http://purl.obolibrary.org/obo/FOODON_03500010) - title: food contact surface - examples: - - value: cellulose acetate [FOODON:03500034] + value: value + description: The street name and building number where the sampling occurred + title: address from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - food - - surface - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001131 - multivalued: true - food_contain_wrap: - name: food_contain_wrap - annotations: - Expected_value: - tag: Expected_value - value: FOODON:03490100 - description: Type of container or wrapping defined by the main container material, - the container form, and the material of the liner lids or ends. Also type of - container or wrapping by form; prefer description by material first, then by - form. This field accepts terms listed under food container or wrapping (http://purl.obolibrary.org/obo/FOODON_03490100) - title: food container or wrapping - examples: - - value: Plastic shrink-pack [FOODON:03490137] + string_serialization: '{integer}{text}' + slot_uri: MIXS:0000218 + multivalued: false + required: false + recommended: false + adj_room: + name: adj_room + description: List of rooms (room number, room name) immediately adjacent to the + sampling room + title: adjacent rooms from_schema: https://w3id.org/mixs-6-2-rc keywords: - - food - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001132 + - adjacent + - room + slot_uri: MIXS:0000219 multivalued: false + range: string required: false recommended: false - food_cooking_proc: - name: food_cooking_proc + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ + structured_pattern: + syntax: ^{room_name};{room_number}$ + interpolated: true + partial_match: true + adjacent_environment: + name: adjacent_environment annotations: Expected_value: tag: Expected_value - value: FOODON:03450002 - description: The transformation of raw food by the application of heat. This field - accepts terms listed under food cooking (http://purl.obolibrary.org/obo/FOODON_03450002) - title: food cooking process + value: ENVO_01001110 or ENVO_00000070 + description: Description of the environmental system or features that are adjacent + to the sampling site. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) + and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple + terms can be separated by pipes + title: environment adjacent to site examples: - - value: food blanching [FOODON:03470175] + - value: estuarine biome [ENVO:01000020] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - food - - process - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001202 + - adjacent + - environment + - site + string_serialization: '{termLabel}{[termID]}' + slot_uri: MIXS:0001121 multivalued: true required: false recommended: false - food_dis_point: - name: food_dis_point - description: 'A reference to a place on the Earth, by its name or by its geographical - location that refers to a distribution point along the food chain. This field - accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448). - Reference: Adam Diamond, James Barham. Moving Food Along the Value Chain: Innovations - in Regional Food Distribution. U.S. Dept. of Agriculture, Agricultural Marketing - Service. Washington, DC. March 2012. http://dx.doi.org/10.9752/MS045.03-2012' - title: food distribution point geographic location + aero_struc: + name: aero_struc + description: Aerospace structures typically consist of thin plates with stiffeners + for the external surfaces, bulkheads and frames to support the shape and fasteners + such as welds, rivets, screws and bolts to hold the components together + title: aerospace structure examples: - - value: 'USA: Delmarva, Peninsula' + - value: plane from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - food - - geographic - - location - slot_uri: MIXS:0001203 - multivalued: true - range: string + slot_uri: MIXS:0000773 + multivalued: false + range: AERO_STRUC_ENUM required: false recommended: false - pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$' - structured_pattern: - syntax: '^{text}: {text}, {text}$' - interpolated: true - partial_match: true - food_dis_point_city: - name: food_dis_point_city + agrochem_addition: + name: agrochem_addition annotations: Expected_value: tag: Expected_value - value: GAZ:00000448 - description: 'A reference to a place on the Earth, by its name or by its geographical - location that refers to a distribution point along the food chain. This field - accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448). - Reference: Adam Diamond, James Barham. Moving Food Along the Value Chain: Innovations - in Regional Food Distribution. U.S. Dept. of Agriculture, Agricultural Marketing - Service. Washington, DC. March 2012. http://dx.doi.org/10.9752/MS045.03-2012' - title: food distribution point geographic location (city) + value: agrochemical name;agrochemical amount;timestamp + Preferred_unit: + tag: Preferred_unit + value: gram, mole per liter, milligram per liter + description: Addition of fertilizers, pesticides, etc. - amount and time of applications + title: history/agrochemical additions examples: - - value: Atlanta[GAZ:00004445] + - value: roundup;5 milligram per liter;2018-06-21 from_schema: https://w3id.org/mixs-6-2-rc keywords: - - food - - geographic - - location - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001204 + - history + string_serialization: '{text};{float} {unit};{timestamp}' + slot_uri: MIXS:0000639 multivalued: true required: false recommended: false - food_harvest_proc: - name: food_harvest_proc - description: A harvesting process is a process which takes in some food material - from an individual or community of plant or animal organisms in a given context - and time, and outputs a precursor or consumable food product. This may include - a part of an organism or the whole, and may involve killing the organism - title: Food harvesting process + air_PM_concen: + name: air_PM_concen + annotations: + Expected_value: + tag: Expected_value + value: particulate matter name;measurement value + description: Concentration of substances that remain suspended in the air, and + comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can + report multiple PM's by entering numeric values preceded by name of PM + title: air particulate matter concentration examples: - - value: hand-picked + - value: PM2.5;10 microgram per cubic meter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - food - - process - slot_uri: MIXS:0001133 + - air + - concentration + - particle + - particulate + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000108 multivalued: true - range: string required: false recommended: false - food_ingredient: - name: food_ingredient + air_flow_impede: + name: air_flow_impede annotations: Expected_value: tag: Expected_value - value: FOODON - description: In this field, please list individual ingredients for multi-component - food [FOODON:00002501] and simple foods that is not captured in food_type. Please - use terms that are present in FoodOn. Multiple terms can be separated by one - or more pipes |, but please consider limiting this list to the top 5 ingredients - listed in order as on the food label. See also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors - title: food ingredient + value: enumeration;obstruction type; distance from sampling device + description: Presence of objects in the area that would influence or impede air + flow through the air filter + title: local air flow impediments examples: - - value: bean (whole) [FOODON:00002753] + - value: obstructed;hay bales; 2 m from_schema: https://w3id.org/mixs-6-2-rc keywords: - - food - - ingredient - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001205 + - air + string_serialization: '[obstructed|unobstructed]; {text}; {measurement value}' + slot_uri: MIXS:0001146 multivalued: true required: false recommended: false - food_name_status: - name: food_name_status - description: A datum indicating that use of a food product name is regulated in - some legal jurisdiction. This field accepts terms listed under food product - name legal status (http://purl.obolibrary.org/obo/FOODON_03530087) - title: food product name legal status - examples: - - value: protected geographic indication [FOODON:03530256] - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - food - - product - - status - slot_uri: MIXS:0001206 - multivalued: false - range: string - required: false - recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ - structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ - interpolated: true - partial_match: true - food_origin: - name: food_origin - description: A reference to a place on the Earth, by its name or by its geographical - location that describes the origin of the food commodity, either in terms of - its cultivation or production. This field accepts terms listed under geographic - location (http://purl.obolibrary.org/obo/GAZ_00000448) - title: food product origin geographic location - examples: - - value: 'USA: Delmarva, Peninsula' - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - food - - geographic - - location - - product - slot_uri: MIXS:0001207 - multivalued: false - range: string - pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$' - structured_pattern: - syntax: '^{text}: {text}, {text}$' - interpolated: true - partial_match: true - food_pack_capacity: - name: food_pack_capacity + air_temp: + name: air_temp annotations: Preferred_unit: tag: Preferred_unit - value: grams - description: The maximum number of product units within a package - title: food package capacity - examples: - - value: 454 grams + value: degree Celsius + description: Temperature of the air at the time of sampling + title: air temperature from_schema: https://w3id.org/mixs-6-2-rc keywords: - - food - - package - slot_uri: MIXS:0001208 + - air + - temperature + slot_uri: MIXS:0000124 multivalued: false range: string - required: false - recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - food_pack_integrity: - name: food_pack_integrity + air_temp_regm: + name: air_temp_regm annotations: Expected_value: tag: Expected_value - value: FOODON:03530218 - description: A term label and term id to describe the state of the packing material - and text to explain the exact condition. This field accepts terms listed under - food packing medium integrity (http://purl.obolibrary.org/obo/FOODON_03530218) - title: food packing medium integrity + value: temperature value;treatment interval and duration + Preferred_unit: + tag: Preferred_unit + value: meter + description: Information about treatment involving an exposure to varying temperatures; + should include the temperature, treatment regimen including how many times the + treatment was repeated, how long each treatment lasted, and the start and end + time of the entire treatment; can include different temperature regimens + title: air temperature regimen examples: - - value: food packing medium compromised [FOODON:00002517] + - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc keywords: - - food - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001209 + - air + - regimen + - temperature + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000551 multivalued: true required: false recommended: false - food_pack_medium: - name: food_pack_medium + al_sat: + name: al_sat annotations: - Expected_value: - tag: Expected_value - value: FOODON:03480020 - description: The medium in which the food is packed for preservation and handling - or the medium surrounding homemade foods, e.g., peaches cooked in sugar syrup. - The packing medium may provide a controlled environment for the food. It may - also serve to improve palatability and consumer appeal. This includes edible - packing media (e.g. fruit juice), gas other than air (e.g. carbon dioxide), - vacuum packed, or packed with aerosol propellant. This field accepts terms under - food packing medium (http://purl.obolibrary.org/obo/FOODON_03480020). Multiple - terms may apply and can be separated by pipes - title: food packing medium + Preferred_unit: + tag: Preferred_unit + value: percentage + description: Aluminum saturation (esp. For tropical soils) + title: extreme_unusual_properties/Al saturation from_schema: https://w3id.org/mixs-6-2-rc keywords: - - food - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001134 - multivalued: true + - extreme + - properties + - saturation + - unusual + slot_uri: MIXS:0000607 + multivalued: false + range: string required: false recommended: false - food_preserv_proc: - name: food_preserv_proc - annotations: - Expected_value: - tag: Expected_value - value: FOODON:03470107 - description: The methods contributing to the prevention or retardation of microbial, - enzymatic or oxidative spoilage and thus to the extension of shelf life. This - field accepts terms listed under food preservation process (http://purl.obolibrary.org/obo/FOODON_03470107) - title: food preservation process - examples: - - value: food slow freezing [FOODON:03470128] + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + al_sat_meth: + name: al_sat_meth + description: Reference or method used in determining Al saturation + title: extreme_unusual_properties/Al saturation method from_schema: https://w3id.org/mixs-6-2-rc keywords: - - food - - process - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001135 - multivalued: true + - extreme + - method + - properties + - saturation + - unusual + slot_uri: MIXS:0000324 + multivalued: false + range: string required: false recommended: false - food_prior_contact: - name: food_prior_contact + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + alkalinity: + name: alkalinity annotations: - Expected_value: - tag: Expected_value - value: FOODON:03530077 - description: The material the food contacted (e.g., was processed in) prior to - packaging. This field accepts terms listed under material of contact prior to - food packaging (http://purl.obolibrary.org/obo/FOODON_03530077). If the proper - descriptor is not listed please use text to describe the material of contact - prior to food packaging - title: material of contact prior to food packaging + Preferred_unit: + tag: Preferred_unit + value: milliequivalent per liter, milligram per liter + description: Alkalinity, the ability of a solution to neutralize acids to the + equivalence point of carbonate or bicarbonate + title: alkalinity examples: - - value: processed in stainless steel container [FOODON:03530081] + - value: 50 milligram per liter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - food - - material - - prior - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001210 - multivalued: true + - alkalinity + slot_uri: MIXS:0000421 + multivalued: false + range: string required: false recommended: false - food_prod: - name: food_prod - description: Descriptors of the food production system or of the agricultural - environment and growing conditions related to the farm production system, such - as wild caught, organic, free-range, industrial, dairy, beef, domestic or cultivated - food production. This field accepts terms listed under food production (http://purl.obolibrary.org/obo/FOODON_03530206). - Multiple terms may apply and can be separated by pipes - title: food production system characteristics - examples: - - value: organic plant cultivation [FOODON:03530253] - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - food - - production - slot_uri: MIXS:0001211 - multivalued: true - range: string - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - food_prod_char: - name: food_prod_char - description: Descriptors of the food production system such as wild caught, free-range, - organic, free-range, industrial, dairy, beef - title: food production characteristics + alkalinity_method: + name: alkalinity_method + description: Method used for alkalinity measurement + title: alkalinity method examples: - - value: wild caught + - value: titration from_schema: https://w3id.org/mixs-6-2-rc keywords: - - food - - production - slot_uri: MIXS:0001136 - multivalued: true + - alkalinity + - method + slot_uri: MIXS:0000298 + multivalued: false range: string required: false recommended: false - food_prod_synonym: - name: food_prod_synonym - description: Other names by which the food product is known by (e.g., regional - or non-English names) - title: food product synonym + alkyl_diethers: + name: alkyl_diethers + description: Concentration of alkyl diethers + title: alkyl diethers examples: - - value: pinot gris + - value: 0.005 mole per liter from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - food - - product - slot_uri: MIXS:0001212 - multivalued: true + slot_uri: MIXS:0000490 + multivalued: false range: string required: false recommended: false - food_product_qual: - name: food_product_qual - description: Descriptors for describing food visually or via other senses, which - is useful for tasks like food inspection where little prior knowledge of how - the food came to be is available. Some terms like "food (frozen)" are both a - quality descriptor and the output of a process. This field accepts terms listed - under food product by quality (http://purl.obolibrary.org/obo/FOODON_00002454) - title: food product by quality - examples: - - value: raw [FOODON:03311126] - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - food - - product - - quality - slot_uri: MIXS:0001213 - multivalued: false - range: string - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - food_product_type: - name: food_product_type + alt: + name: alt annotations: - Expected_value: - tag: Expected_value - value: FOODON:00001002 or FOODON:03309997 - description: A food product type is a class of food products that is differentiated - by its food composition (e.g., single- or multi-ingredient), processing and/or - consumption characteristics. This does not include brand name products but it - may include generic food dish categories. This field accepts terms under food - product type (http://purl.obolibrary.org/obo/FOODON:03400361). For terms related - to food product for an animal, consult food product for animal (http://purl.obolibrary.org/obo/FOODON_03309997). - If the proper descriptor is not listed please use text to describe the food - type. Multiple terms can be separated by one or more pipes - title: food product type + Preferred_unit: + tag: Preferred_unit + value: meter + description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric + balloons and heights of places such as atmospheric layers and clouds. It is + used to measure the height of an object which is above the earth's surface. + In this context, the altitude measurement is the vertical distance between the + earth's surface above sea level and the sampled position in the air + title: altitude + examples: + - value: 100 meter + in_subset: + - environment from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - food - - product - - type - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001184 + slot_uri: MIXS:0000094 multivalued: false - food_quality_date: - name: food_quality_date + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + aminopept_act: + name: aminopept_act annotations: - Expected_value: - tag: Expected_value - value: enumeration, date - description: The date recommended for the use of the product while at peak quality, - this date is not a reflection of safety unless used on infant formula this date - is not a reflection of safety and is typically labeled on a food product as - "best if used by," best by," "use by," or "freeze by." - title: food quality date + Preferred_unit: + tag: Preferred_unit + value: mole per liter per hour + description: Measurement of aminopeptidase activity + title: aminopeptidase activity examples: - - value: best by 2020-05-24 + - value: 0.269 mole per liter per hour from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - date - - food - - quality - string_serialization: '[best by|best if used by|freeze by|use by]; date' - slot_uri: MIXS:0001178 + slot_uri: MIXS:0000172 multivalued: false + range: string required: false recommended: false - food_source: - name: food_source + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + ammonium: + name: ammonium annotations: - Expected_value: - tag: Expected_value - value: FOODON term - description: Type of plant or animal from which the food product or its major - ingredient is derived or a chemical food source [FDA CFSAN 1995] - title: food source + Preferred_unit: + tag: Preferred_unit + value: micromole per liter, milligram per liter, parts per million + description: Concentration of ammonium in the sample + title: ammonium + examples: + - value: 1.5 milligram per liter from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - food - - source - string_serialization: '{termLabel} [{termID}]' - slot_uri: MIXS:0001139 + slot_uri: MIXS:0000427 multivalued: false - food_source_age: - name: food_source_age + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + amniotic_fluid_color: + name: amniotic_fluid_color + description: Specification of the color of the amniotic fluid sample + title: amniotic fluid/color + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000276 + multivalued: false + range: string + required: false + recommended: false + amount_light: + name: amount_light annotations: Preferred_unit: tag: Preferred_unit - value: days - description: The age of the food source host organim. Depending on the type of - host organism, age may be more appropriate to report in days, weeks, or years - title: food source age - comments: - - ISO 8601 period or measurement value? - examples: - - value: 6 months + value: lux, lumens per square meter + description: The unit of illuminance and luminous emittance, measuring luminous + flux per unit area + title: amount of light from_schema: https://w3id.org/mixs-6-2-rc keywords: - - age - - food - - source - slot_uri: MIXS:0001251 + - light + slot_uri: MIXS:0000140 + multivalued: false range: string required: false recommended: false @@ -7802,43 +6125,35 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - food_trace_list: - name: food_trace_list - description: The FDA is proposing to establish additional traceability recordkeeping - requirements (beyond what is already required in existing regulations) for persons - who manufacture, process, pack, or hold foods the Agency has designated for - inclusion on the Food Traceability List. The Food Traceability List (FTL) identifies - the foods for which the additional traceability records described in the proposed - rule would be required. The term Food Traceability List (FTL) refers not only - to the foods specifically listed (https://www.fda.gov/media/142303/download), - but also to any foods that contain listed foods as ingredients - title: food traceability list category + ances_data: + name: ances_data + description: Information about either pedigree or other ancestral information + description (e.g. parental variety in case of mutant or selection), e.g. A/3*B + (meaning [(A x B) x B] x B) + title: ancestral data examples: - - value: tropical tree fruits + - value: A/3*B from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - food - slot_uri: MIXS:0001214 + slot_uri: MIXS:0000247 multivalued: false - range: FOOD_TRACE_LIST_ENUM + range: string required: false recommended: false - food_trav_mode: - name: food_trav_mode - description: A descriptor for the method of movement of food commodity along the - food distribution system. This field accepts terms listed under travel mode - (http://purl.obolibrary.org/obo/GENEPIO_0001064). If the proper descrptor is - not listed please use text to describe the mode of travel. Multiple terms can - be separated by one or more pipes - title: food shipping transportation method + anim_water_method: + name: anim_water_method + description: Description of the equipment or method used to distribute water to + livestock. This field accepts termed listed under water delivery equipment (http://opendata.inra.fr/EOL/EOL_0001653). + Multiple terms can be separated by pipes + title: animal water delivery method examples: - - value: train travel [GENEPIO:0001060] + - value: water trough [EOL:0001618] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - food + - animal + - delivery - method - - transport - slot_uri: MIXS:0001137 + - water + slot_uri: MIXS:0001115 multivalued: true range: string required: false @@ -7848,244 +6163,284 @@ slots: syntax: ^{termLabel} \[{termID}\]$ interpolated: true partial_match: true - food_trav_vehic: - name: food_trav_vehic - annotations: - Expected_value: - tag: Expected_value - value: ENVO:01000604 - description: A descriptor for the mobile machine which is used to transport food - commodities along the food distribution system. This field accepts terms listed - under vehicle (http://purl.obolibrary.org/obo/ENVO_01000604). If the proper - descrptor is not listed please use text to describe the mode of travel. Multiple - terms can be separated by one or more pipes - title: food shipping transportation vehicle + animal_am: + name: animal_am + description: The name(s) (generic or brand) of the antimicrobial(s) given to the + food animal within the last 30 days + title: food animal antimicrobial examples: - - value: aircraft [ENVO:01001488]|car [ENVO:01000605] + - value: tetracycline from_schema: https://w3id.org/mixs-6-2-rc keywords: + - animal + - antimicrobial - food - - transport - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001138 - multivalued: true + slot_uri: MIXS:0001243 + multivalued: false + range: string required: false recommended: false - food_treat_proc: - name: food_treat_proc + animal_am_dur: + name: animal_am_dur annotations: Expected_value: tag: Expected_value - value: FOODON:03460111 - description: Used to specifically characterize a food product based on the treatment - or processes applied to the product or any indexed ingredient. The processes - include adding, substituting or removing components or modifying the food or - component, e.g., through fermentation. Multiple values can be assigned. This - fields accepts terms listed under food treatment process (http://purl.obolibrary.org/obo/FOODON_03460111) - title: food treatment process + value: value + description: The duration of time (days) that the antimicrobial was administered + to the food animal + title: food animal antimicrobial duration examples: - - value: gluten removal process [FOODON:03460750] + - value: 3 days from_schema: https://w3id.org/mixs-6-2-rc keywords: + - animal + - antimicrobial + - duration - food - - process - - treatment - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001140 - multivalued: true + - period + string_serialization: '{float} {day}' + slot_uri: MIXS:0001244 + multivalued: false required: false recommended: false - freq_clean: - name: freq_clean - description: The number of times the sample location is cleaned. Frequency of - cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually - title: frequency of cleaning + animal_am_freq: + name: animal_am_freq + description: The frequency per day that the antimicrobial was adminstered to the + food animal + title: food animal antimicrobial frequency examples: - - value: Daily + - value: '1.5' from_schema: https://w3id.org/mixs-6-2-rc keywords: + - animal + - antimicrobial + - food - frequency - slot_uri: MIXS:0000226 - multivalued: false - range: FREQ_CLEAN_ENUM + slot_uri: MIXS:0001245 + range: float required: false recommended: false - freq_cook: - name: freq_cook - description: The number of times a meal is cooked per week - title: frequency of cooking + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + animal_am_route: + name: animal_am_route + description: The route by which the antimicrobial is adminstered into the body + of the food animal + title: food animal antimicrobial route of administration + examples: + - value: oral-feed from_schema: https://w3id.org/mixs-6-2-rc keywords: - - frequency - slot_uri: MIXS:0000227 + - administration + - animal + - antimicrobial + - food + - route + slot_uri: MIXS:0001246 multivalued: false range: string required: false recommended: false - pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{integer} {text}$ - interpolated: true - partial_match: true - fungicide_regm: - name: fungicide_regm - annotations: - Preferred_unit: - tag: Preferred_unit - value: gram, mole per liter, milligram per liter - description: Information about treatment involving use of fungicides; should include - the name of fungicide, amount administered, treatment regimen including how - many times the treatment was repeated, how long each treatment lasted, and the - start and end time of the entire treatment; can include multiple fungicide regimens - title: fungicide regimen + animal_am_use: + name: animal_am_use + description: The prescribed intended use of or the condition treated by the antimicrobial + given to the food animal by any route of administration + title: food animal antimicrobial intended use examples: - - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: shipping fever from_schema: https://w3id.org/mixs-6-2-rc keywords: - - regimen - slot_uri: MIXS:0000557 - multivalued: true + - animal + - antimicrobial + - food + - use + slot_uri: MIXS:0001247 + multivalued: false range: string - furniture: - name: furniture - description: The types of furniture present in the sampled room - title: furniture + required: false + recommended: false + animal_body_cond: + name: animal_body_cond + description: Body condition scoring is a production management tool used to evaluate + overall health and nutritional needs of a food animal. Because there are different + scoring systems, this field is restricted to three categories + title: food animal body condition examples: - - value: chair + - value: under conditioned from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000807 + keywords: + - animal + - body + - condition + - food + slot_uri: MIXS:0001248 multivalued: false - range: FURNITURE_ENUM + range: ANIMAL_BODY_COND_ENUM required: false recommended: false - gaseous_environment: - name: gaseous_environment + animal_diet: + name: animal_diet annotations: - Preferred_unit: - tag: Preferred_unit - value: micromole per liter - description: Use of conditions with differing gaseous environments; should include - the name of gaseous compound, amount administered, treatment duration, interval - and total experimental duration; can include multiple gaseous environment regimens - title: gaseous environment + Expected_value: + tag: Expected_value + value: text or FOODON_03309997 + description: If the isolate is from a food animal, the type of diet eaten by the + food animal. Please list the main food staple and the setting, if appropriate. For + a list of acceptable animal feed terms or categories, please see http://www.feedipedia.org. Multiple + terms may apply and can be separated by pipes |Food product for animal covers + foods intended for consumption by domesticated animals. Consult http://purl.obolibrary.org/obo/FOODON_03309997. + If the proper descriptor is not listed please use text to describe the food + type. Multiple terms can be separated by one or more pipes. If the proper descriptor + is not listed please use text to describe the food product type + title: food animal source diet examples: - - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: Hay [FOODON:03301763] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - environment - slot_uri: MIXS:0000558 + - animal + - diet + - food + - source + string_serialization: '{text}' + slot_uri: MIXS:0001130 multivalued: true - range: string - gaseous_substances: - name: gaseous_substances + required: false + recommended: false + animal_feed_equip: + name: animal_feed_equip annotations: Expected_value: tag: Expected_value - value: gaseous substance name;measurement value - Preferred_unit: - tag: Preferred_unit - value: micromole per liter - description: Amount or concentration of substances such as hydrogen sulfide, carbon - dioxide, methane, etc.; can include multiple substances - title: gaseous substances - from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000661 - multivalued: true - required: false - recommended: false - gastrointest_disord: - name: gastrointest_disord - description: History of gastrointestinal tract disorders; can include multiple - disorders. History of blood disorders; can include multiple disorders. The - terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77) - title: gastrointestinal tract disorder + value: EOL:0001757 + description: Description of the feeding equipment used for livestock. This field + accepts terms listed under feed delivery (http://opendata.inra.fr/EOL/EOL_0001757). + Multiple terms can be separated by pipes + title: animal feeding equipment + examples: + - value: self feeding [EOL:0001645]| straight feed trough [EOL:0001661] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - disorder - slot_uri: MIXS:0000280 + - animal + - equipment + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0001113 multivalued: true - range: string required: false recommended: false - gender_restroom: - name: gender_restroom - description: The gender type of the restroom - title: gender of restroom + animal_group_size: + name: animal_group_size + description: The number of food animals of the same species that are maintained + together as a unit, i.e. a herd or flock + title: food animal group size examples: - - value: male + - value: '80' from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000808 + keywords: + - animal + - food + - size + slot_uri: MIXS:0001129 multivalued: false - range: GENDER_RESTROOM_ENUM + range: integer required: false recommended: false - genetic_mod: - name: genetic_mod - annotations: - Expected_value: - tag: Expected_value - value: PMID, DOI, URL or text - description: Genetic modifications of the genome of an organism, which may occur - naturally by spontaneous mutation, or be introduced by some experimental means, - e.g. specification of a transgene or the gene knocked-out or details of transient - transfection - title: genetic modification + animal_housing: + name: animal_housing + description: Description of the housing system of the livestock. This field accepts + terms listed under terrestrial management housing system (http://opendata.inra.fr/EOL/EOL_0001605) + title: animal housing system examples: - - value: aox1A transgenic + - value: pen rearing system [EOL:0001636] from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000859 - multivalued: false + keywords: + - animal + slot_uri: MIXS:0001180 + multivalued: true + range: string required: false recommended: false - geo_loc_name: - name: geo_loc_name - description: The geographical origin of the sample as defined by the country or - sea name followed by specific region name. Country or sea names should be chosen - from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology - (http://purl.bioontology.org/ontology/GAZ) - title: geographic location (country and/or sea,region) + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + animal_intrusion: + name: animal_intrusion + description: Identification of animals intruding on the sample or sample site + including invertebrates (such as pests or pollinators) and vertebrates (such + as wildlife or domesticated animals). This field accepts terms under organism + (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification + numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms + can be separated by pipes + title: animal intrusion near sample source examples: - - value: 'USA: Maryland, Bethesda' - in_subset: - - environment + - value: Thripidae [NCBITaxon:45053] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - geographic - - location - slot_uri: MIXS:0000010 - multivalued: false + - animal + - sample + - source + slot_uri: MIXS:0001114 + multivalued: true range: string - required: true - pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$' + required: false + recommended: false + pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ structured_pattern: - syntax: '^{text}: {text}, {text}$' + syntax: ^({termLabel} \[{termID}\])|{integer}$ interpolated: true partial_match: true - gestation_state: - name: gestation_state - description: Specification of the gestation state - title: amniotic fluid/gestation state + animal_sex: + name: animal_sex + description: The sex and reproductive status of the food animal + title: food animal source sex category + examples: + - value: castrated male from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000272 + keywords: + - animal + - food + - source + slot_uri: MIXS:0001249 multivalued: false - range: string + range: ANIMAL_SEX_ENUM required: false recommended: false - glucosidase_act: - name: glucosidase_act + annot: + name: annot + annotations: + Expected_value: + tag: Expected_value + value: name of tool or pipeline used, or annotation source description + description: Tool used for annotation, or for cases where annotation was provided + by a community jamboree or model organism database rather than by a specific + submitter + title: annotation + examples: + - value: prokka + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + string_serialization: '{text}' + slot_uri: MIXS:0000059 + multivalued: false + annual_precpt: + name: annual_precpt annotations: Preferred_unit: tag: Preferred_unit - value: mol per liter per hour - description: Measurement of glucosidase activity - title: glucosidase activity - examples: - - value: 5 mol per liter per hour + value: millimeter + description: The average of all annual precipitation values known, or an estimated + equivalent value derived by such methods as regional indexes or Isohyetal maps + title: mean annual precipitation from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000137 + keywords: + - mean + slot_uri: MIXS:0000644 multivalued: false range: string required: false @@ -8096,390 +6451,414 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - gravidity: - name: gravidity - description: Whether or not subject is gravid, and if yes date due or date post-conception, - specifying which is used - title: gravidity + annual_temp: + name: annual_temp + annotations: + Preferred_unit: + tag: Preferred_unit + value: degree Celsius + description: Mean annual temperature + title: mean annual temperature examples: - - value: yes;due date:2018-05-11 + - value: 12.5 degree Celsius from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{boolean};{timestamp}' - slot_uri: MIXS:0000875 + keywords: + - mean + - temperature + slot_uri: MIXS:0000642 multivalued: false + range: string required: false recommended: false - gravity: - name: gravity + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + antibiotic_regm: + name: antibiotic_regm annotations: Expected_value: tag: Expected_value - value: gravity factor value;treatment interval and duration + value: antibiotic name;antibiotic amount;treatment interval and duration Preferred_unit: tag: Preferred_unit - value: meter per square second, g - description: Information about treatment involving use of gravity factor to study - various types of responses in presence, absence or modified levels of gravity; - treatment regimen including how many times the treatment was repeated, how long - each treatment lasted, and the start and end time of the entire treatment; can - include multiple treatments - title: gravity + value: milligram + description: Information about treatment involving antibiotic administration; + should include the name of antibiotic, amount administered, treatment regimen + including how many times the treatment was repeated, how long each treatment + lasted, and the start and end time of the entire treatment; can include multiple + antibiotic regimens + title: antibiotic regimen examples: - - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000559 + keywords: + - regimen + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000553 multivalued: true required: false recommended: false - growth_facil: - name: growth_facil + api: + name: api annotations: - Expected_value: - tag: Expected_value - value: free text or CO - description: 'Type of facility where the sampled plant was grown; controlled vocabulary: - growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively - use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research' - title: growth facility + Preferred_unit: + tag: Preferred_unit + value: degrees API + description: 'API gravity is a measure of how heavy or light a petroleum liquid + is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. + 31.1 API)' + title: API gravity examples: - - value: Growth chamber [CO_715:0000189] + - value: 31.1 API from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - facility - - growth - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001043 + slot_uri: MIXS:0000157 multivalued: false - required: false - recommended: false - growth_habit: - name: growth_habit - description: Characteristic shape, appearance or growth form of a plant species - title: growth habit + range: string + required: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + arch_struc: + name: arch_struc + description: An architectural structure is a human-made, free-standing, immobile + outdoor construction + title: architectural structure examples: - - value: spreading + - value: shed from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - growth - slot_uri: MIXS:0001044 + slot_uri: MIXS:0000774 multivalued: false - range: GROWTH_HABIT_ENUM + range: ARCH_STRUC_ENUM required: false recommended: false - growth_hormone_regm: - name: growth_hormone_regm + area_samp_size: + name: area_samp_size annotations: Expected_value: tag: Expected_value - value: growth hormone name;growth hormone amount;treatment interval and duration + value: measurement value Preferred_unit: tag: Preferred_unit - value: gram, mole per liter, milligram per liter - description: Information about treatment involving use of growth hormones; should - include the name of growth hormone, amount administered, treatment regimen including - how many times the treatment was repeated, how long each treatment lasted, and - the start and end time of the entire treatment; can include multiple growth - hormone regimens - title: growth hormone regimen + value: centimeter + description: The total amount or size (volume (ml), mass (g) or area (m2) ) of + sample collected + title: area sampled size examples: - - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: 12 centimeter x 12 centimeter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - growth - - regimen - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000560 - multivalued: true + - area + - sample + - size + string_serialization: '{integer} {unit} x {integer} {unit}' + slot_uri: MIXS:0001255 + multivalued: false required: false recommended: false - growth_medium: - name: growth_medium - description: A liquid or gel containing nutrients, salts, and other factors formulated - to support the growth of microorganisms, cells, or plants (National Cancer Institute - Thesaurus). The name of the medium used to grow the microorganism - title: growth medium - examples: - - value: LB broth + aromatics_pc: + name: aromatics_pc + annotations: + Preferred_unit: + tag: Preferred_unit + value: percent + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis + method that divides crude oil components according to their polarizability + and polarity. There are three main methods to obtain SARA results. The most + popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: + https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' + title: aromatics wt% from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - growth - slot_uri: MIXS:0001108 + slot_uri: MIXS:0000133 multivalued: false range: string - required: false - recommended: false - gynecologic_disord: - name: gynecologic_disord - description: History of gynecological disorders; can include multiple disorders. - The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - female reproductive system disease (https://disease-ontology.org/?id=DOID:229) - title: gynecological disorder + recommended: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{name};{float} {unit}$ + interpolated: true + partial_match: true + asphaltenes_pc: + name: asphaltenes_pc + annotations: + Preferred_unit: + tag: Preferred_unit + value: percent + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis + method that divides crude oil components according to their polarizability + and polarity. There are three main methods to obtain SARA results. The most + popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: + https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' + title: asphaltenes wt% from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - disorder - slot_uri: MIXS:0000288 - multivalued: true + slot_uri: MIXS:0000135 + multivalued: false range: string - required: false - recommended: false - hall_count: - name: hall_count - description: The total count of hallways and cooridors in the built structure - title: hallway/corridor count + recommended: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{name};{float} {unit}$ + interpolated: true + partial_match: true + assembly_name: + name: assembly_name + annotations: + Expected_value: + tag: Expected_value + value: name and version of assembly + description: Name/version of the assembly provided by the submitter that is used + in the genome browsers and in the community + title: assembly name + examples: + - value: HuRef, JCVI_ISG_i3_1.0 + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - corridor - - count - - hallway - slot_uri: MIXS:0000228 + string_serialization: '{text} {text}' + slot_uri: MIXS:0000057 multivalued: false - range: integer - required: false - recommended: false - handidness: - name: handidness - description: The handidness of the individual sampled - title: handidness + assembly_qual: + name: assembly_qual + annotations: + Expected_value: + tag: Expected_value + value: enumeration + description: 'The assembly quality category is based on sets of criteria outlined + for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, + contiguous sequence per replicon without gaps or ambiguities with a consensus + error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments + where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes + and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no + review of assembly other than reporting of standard assembly statistics. Low + Quality Draft:Many fragments with little to no review of assembly other than + reporting of standard assembly statistics. Assembly statistics include, but + are not limited to total assembly size, number of contigs, contig N50/L50, and + maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence + per replicon without gaps or ambiguities, with extensive manual review and editing + to annotate putative gene functions and transcriptional units. High-quality + draft genome: One or multiple fragments, totaling 90% of the expected genome + or replicon sequence or predicted complete. Genome fragment(s): One or multiple + fragments, totalling < 90% of the expected genome or replicon sequence, or for + which no genome size could be estimated' + title: assembly quality examples: - - value: right handedness + - value: High-quality draft genome + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000809 + keywords: + - quality + string_serialization: '[Finished genome|High-quality draft genome|Medium-quality + draft genome|Low-quality draft genome|Genome fragment(s)]' + slot_uri: MIXS:0000056 multivalued: false - range: HANDIDNESS_ENUM - required: false - recommended: false - hc_produced: - name: hc_produced - description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, - etc). If "other" is specified, please propose entry in "additional info" field - title: hydrocarbon type produced + assembly_software: + name: assembly_software + description: Tool(s) used for assembly, including version number and parameters + title: assembly software examples: - - value: Gas + - value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - hydrocarbon - - type - slot_uri: MIXS:0000989 + - software + slot_uri: MIXS:0000058 multivalued: false - range: HC_PRODUCED_ENUM - required: true - hcr: - name: hcr - description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR - defined as a natural environmental feature containing large amounts of hydrocarbons - at high concentrations potentially suitable for commercial exploitation. This - term should not be confused with the Hydrocarbon Occurrence term which also - includes hydrocarbon-rich environments with currently limited commercial interest - such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose - entry in "additional info" field - title: hydrocarbon resource type + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{software};{version};{parameters}$ + interpolated: true + partial_match: true + associated_resource: + name: associated_resource + annotations: + Expected_value: + tag: Expected_value + value: reference to resource + description: A related resource that is referenced, cited, or otherwise associated + to the sequence + title: relevant electronic resources examples: - - value: Oil Sand + - value: http://www.earthmicrobiome.org/ + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - hydrocarbon - resource - - type - slot_uri: MIXS:0000988 - multivalued: false - range: HCR_ENUM - required: true - hcr_fw_salinity: - name: hcr_fw_salinity + string_serialization: '{PMID}|{DOI}|{URL}' + slot_uri: MIXS:0000091 + multivalued: true + recommended: true + association_duration: + name: association_duration annotations: Preferred_unit: tag: Preferred_unit - value: milligram per liter - description: Original formation water salinity (prior to secondary recovery e.g. - Waterflooding) expressed as TDS - title: formation water salinity + value: year, day, hour + description: Time spent in host of the symbiotic organism at the time of sampling; + relevant scale depends on symbiotic organism and study + title: duration of association with the host from_schema: https://w3id.org/mixs-6-2-rc keywords: - - salinity - - water - slot_uri: MIXS:0000406 + - duration + - host + - host. + - period + slot_uri: MIXS:0001299 multivalued: false range: string - recommended: true + required: false + recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - hcr_geol_age: - name: hcr_geol_age - description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). - If "other" is specified, please propose entry in "additional info" field' - title: hydrocarbon resource geological age + atmospheric_data: + name: atmospheric_data + annotations: + Expected_value: + tag: Expected_value + value: atmospheric data name;measurement value + description: Measurement of atmospheric data; can include multiple data + title: atmospheric data examples: - - value: Silurian + - value: wind speed;9 knots from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - age - - hydrocarbon - - resource - slot_uri: MIXS:0000993 - multivalued: false - range: SHARED_ENUM_5 - recommended: true - hcr_pressure: - name: hcr_pressure + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0001097 + multivalued: true + required: false + recommended: false + avg_dew_point: + name: avg_dew_point annotations: Preferred_unit: tag: Preferred_unit - value: atmosphere, kilopascal - description: Original pressure of the hydrocarbon resource - title: hydrocarbon resource original pressure + value: degree Celsius + description: The average of dew point measures taken at the beginning of every + hour over a 24 hour period on the sampling day + title: average dew point + examples: + - value: 25.5 degree Celsius from_schema: https://w3id.org/mixs-6-2-rc keywords: - - hydrocarbon - - pressure - - resource - slot_uri: MIXS:0000395 + - average + slot_uri: MIXS:0000141 multivalued: false range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{float} *- *{float} {unit}$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - hcr_temp: - name: hcr_temp + avg_occup: + name: avg_occup + description: Daily average occupancy of room. Indicate the number of person(s) + daily occupying the sampling room + title: average daily occupancy + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - average + slot_uri: MIXS:0000775 + multivalued: false + range: float + required: false + recommended: false + avg_temp: + name: avg_temp annotations: Preferred_unit: tag: Preferred_unit value: degree Celsius - description: Original temperature of the hydrocarbon resource - title: hydrocarbon resource original temperature + description: The average of temperatures taken at the beginning of every hour + over a 24 hour period on the sampling day + title: average temperature examples: - - value: 150-295 degree Celsius + - value: 12.5 degree Celsius from_schema: https://w3id.org/mixs-6-2-rc keywords: - - hydrocarbon - - resource + - average - temperature - slot_uri: MIXS:0000393 + slot_uri: MIXS:0000142 multivalued: false range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{float} *- *{float} {unit}$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - heat_cool_type: - name: heat_cool_type - description: Methods of conditioning or heating a room or building - title: heating and cooling system type + bac_prod: + name: bac_prod + annotations: + Preferred_unit: + tag: Preferred_unit + value: milligram per cubic meter per day + description: Bacterial production in the water column measured by isotope uptake + title: bacterial production examples: - - value: heat pump + - value: 5 milligram per cubic meter per day from_schema: https://w3id.org/mixs-6-2-rc keywords: - - type - slot_uri: MIXS:0000766 - multivalued: true - range: HEAT_COOL_TYPE_ENUM - required: true - heat_deliv_loc: - name: heat_deliv_loc - description: The location of heat delivery within the room - title: heating delivery locations - examples: - - value: north - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - delivery - - location - - locations - slot_uri: MIXS:0000810 - multivalued: false - range: SHARED_ENUM_0 - required: false - recommended: false - heat_sys_deliv_meth: - name: heat_sys_deliv_meth - description: The method by which the heat is delivered through the system - title: heating system delivery method - examples: - - value: radiant - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - delivery - - method - slot_uri: MIXS:0000812 - multivalued: false - range: HEAT_SYS_DELIV_METH_ENUM - required: false - recommended: false - heat_system_id: - name: heat_system_id - description: The heating system identifier - title: heating system identifier - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - identifier - slot_uri: MIXS:0000833 + - production + slot_uri: MIXS:0000683 multivalued: false - range: integer + range: string required: false recommended: false - heavy_metals: - name: heavy_metals + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + bac_resp: + name: bac_resp annotations: - Expected_value: - tag: Expected_value - value: heavy metal name;measurement value unit Preferred_unit: tag: Preferred_unit - value: microgram per gram - description: Heavy metals present in the sequenced sample and their concentrations. - For multiple heavy metals and concentrations, add multiple copies of this field - title: extreme_unusual_properties/heavy metals + value: milligram per cubic meter per day, micromole oxygen per liter per hour + description: Measurement of bacterial respiration in the water column + title: bacterial respiration examples: - - value: mercury;0.09 micrograms per gram - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - extreme - - properties - - unusual - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000652 - multivalued: true - required: false - recommended: false - heavy_metals_meth: - name: heavy_metals_meth - description: Reference or method used in determining heavy metals - title: extreme_unusual_properties/heavy metals method + - value: 300 micromole oxygen per liter per hour from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - extreme - - method - - properties - - unusual - slot_uri: MIXS:0000343 + slot_uri: MIXS:0000684 multivalued: false range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - height_carper_fiber: - name: height_carper_fiber - annotations: - Preferred_unit: - tag: Preferred_unit - value: centimeter - description: The average carpet fiber height in the indoor environment - title: height carpet fiber mat + bacteria_carb_prod: + name: bacteria_carb_prod + description: Measurement of bacterial carbon production + title: bacterial carbon production + examples: + - value: 2.53 microgram per liter per hour from_schema: https://w3id.org/mixs-6-2-rc keywords: - - height - slot_uri: MIXS:0000167 + - carbon + - production + slot_uri: MIXS:0000173 multivalued: false range: string required: false @@ -8490,164 +6869,164 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - herbicide_regm: - name: herbicide_regm + bacterial_density: + name: bacterial_density annotations: Preferred_unit: tag: Preferred_unit - value: gram, mole per liter, milligram per liter - description: Information about treatment involving use of herbicides; information - about treatment involving use of growth hormones; should include the name of - herbicide, amount administered, treatment regimen including how many times the - treatment was repeated, how long each treatment lasted, and the start and end - time of the entire treatment; can include multiple regimens - title: herbicide regimen + value: colony forming units per milliliter; colony forming units per gram + of dry weight + description: Number of bacteria in sample, as defined by bacteria density (http://purl.obolibrary.org/obo/GENEPIO_0000043) + title: bacteria density examples: - - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - regimen - slot_uri: MIXS:0000561 - multivalued: true - range: string - horizon_meth: - name: horizon_meth - description: Reference or method used in determining the horizon - title: horizon method + - value: 10 colony forming units per gram dry weight from_schema: https://w3id.org/mixs-6-2-rc keywords: - - horizon - - method - slot_uri: MIXS:0000321 + - density + slot_uri: MIXS:0001194 multivalued: false range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - host_age: - name: host_age + barometric_press: + name: barometric_press annotations: Preferred_unit: tag: Preferred_unit - value: year, day, hour - description: Age of host at the time of sampling; relevant scale depends on species - and study, e.g. Could be seconds for amoebae or centuries for trees - title: host age + value: millibar + description: Force per unit area exerted against a surface by the weight of air + above that surface + title: barometric pressure + examples: + - value: 5 millibar from_schema: https://w3id.org/mixs-6-2-rc keywords: - - age - - host - - host. - slot_uri: MIXS:0000255 + - pressure + slot_uri: MIXS:0000096 multivalued: false range: string + required: false + recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - host_body_habitat: - name: host_body_habitat - description: Original body habitat where the sample was obtained from - title: host body habitat + basin: + name: basin + description: Name of the basin (e.g. Campos) + title: basin name + examples: + - value: Campos from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - body - - habitat - - host - - host. - slot_uri: MIXS:0000866 + slot_uri: MIXS:0000290 multivalued: false range: string + required: true + bathroom_count: + name: bathroom_count + description: The number of bathrooms in the building + title: bathroom count + examples: + - value: '1' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - count + slot_uri: MIXS:0000776 + multivalued: false + range: integer required: false recommended: false - host_body_mass_index: - name: host_body_mass_index - annotations: - Preferred_unit: - tag: Preferred_unit - value: kilogram per square meter - description: Body mass index, calculated as weight/(height)squared - title: host body-mass index + bedroom_count: + name: bedroom_count + description: The number of bedrooms in the building + title: bedroom count examples: - - value: 22 kilogram per square meter + - value: '2' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - slot_uri: MIXS:0000317 + - count + slot_uri: MIXS:0000777 multivalued: false - range: string + range: integer required: false recommended: false + benzene: + name: benzene + annotations: + Preferred_unit: + tag: Preferred_unit + value: milligram per liter, parts per million + description: Concentration of benzene in the sample + title: benzene + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000153 + multivalued: false + range: string + recommended: true pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - host_body_product: - name: host_body_product - annotations: - Expected_value: - tag: Expected_value - value: FMA or UBERON - description: Substance produced by the body, e.g. Stool, mucus, where the sample - was obtained from. Use terms from the foundational model of anatomy ontology - (fma) or Uber-anatomy ontology (UBERON) - title: host body product + bin_param: + name: bin_param + description: The parameters that have been applied during the extraction of genomes + from metagenomic datasets + title: binning parameters examples: - - value: mucus [FMA:66938] + - value: coverage + description: was 'coverage and kmer' + - value: kmer + description: was coverage and kmer + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - body - - host - - host. - - product - string_serialization: '{termLabel} [{termID}]' - slot_uri: MIXS:0000888 - multivalued: false - required: false - recommended: false - host_body_site: - name: host_body_site + - parameter + slot_uri: MIXS:0000077 + range: BIN_PARAM_ENUM + bin_software: + name: bin_software annotations: Expected_value: tag: Expected_value - value: FMA or UBERON - description: Name of body site where the sample was obtained from, such as a specific - organ or tissue (tongue, lung etc...). Use terms from the foundational model - of anatomy ontology (fma) or the Uber-anatomy ontology (UBERON) - title: host body site + value: names and versions of software(s) used + description: Tool(s) used for the extraction of genomes from metagenomic datasets, + where possible include a product ID (PID) of the tool(s) used + title: binning software + examples: + - value: MetaCluster-TA (RRID:SCR_004599), MaxBin (biotools:maxbin) + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - body - - host - - host. - - site - string_serialization: '{termLabel} [{termID}]' - slot_uri: MIXS:0000867 + - software + string_serialization: '{software};{version}{PID}' + slot_uri: MIXS:0000078 multivalued: false - required: false - recommended: false - host_body_temp: - name: host_body_temp + biochem_oxygen_dem: + name: biochem_oxygen_dem annotations: Preferred_unit: tag: Preferred_unit - value: degree Celsius - description: Core body temperature of the host when sample was collected - title: host body temperature + value: milligram per liter + description: Amount of dissolved oxygen needed by aerobic biological organisms + in a body of water to break down organic material present in a given water sample + at certain temperature over a specific time period + title: biochemical oxygen demand from_schema: https://w3id.org/mixs-6-2-rc keywords: - - body - - host - - host. - - temperature - slot_uri: MIXS:0000274 + - oxygen + slot_uri: MIXS:0000653 multivalued: false range: string required: false @@ -8658,631 +7037,537 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - host_cellular_loc: - name: host_cellular_loc - description: 'The localization of the symbiotic host organism within the host - from which it was sampled: e.g. intracellular if the symbiotic host organism - is localized within the cells or extracellular if the symbiotic host organism - is localized outside of cells' - title: host cellular location + biocide: + name: biocide + annotations: + Expected_value: + tag: Expected_value + value: name;name;timestamp + description: List of biocides (commercial name of product and supplier) and date + of administration + title: biocide administration examples: - - value: extracellular - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - location - slot_uri: MIXS:0001313 - range: HOST_CELLULAR_LOC_ENUM - recommended: true - host_color: - name: host_color - description: The color of host - title: host color + - value: ALPHA 1427;Baker Hughes;2008-01-23 from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - slot_uri: MIXS:0000260 + - administration + string_serialization: '{text};{text};{timestamp}' + slot_uri: MIXS:0001011 multivalued: false - range: string - required: false - recommended: false - host_common_name: - name: host_common_name + recommended: true + biocide_admin_method: + name: biocide_admin_method annotations: + Expected_value: + tag: Expected_value + value: measurement value;frequency;duration;duration Preferred_unit: tag: Preferred_unit - value: '' - description: Common name of the host - title: host common name + value: milligram per liter + description: Method of biocide administration (dose, frequency, duration, time + elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 + days) + title: biocide administration method from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - slot_uri: MIXS:0000248 + - administration + - method + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}' + slot_uri: MIXS:0000456 multivalued: false - range: string - host_dependence: - name: host_dependence - description: Type of host dependence for the symbiotic host organism to its host - title: host dependence + recommended: true + biocide_used: + name: biocide_used + annotations: + Expected_value: + tag: Expected_value + value: commercial name of biocide, active ingredient in biocide or class of + biocide + description: Substance intended for preventing, neutralizing, destroying, repelling, + or mitigating the effects of any pest or microorganism; that inhibits the growth, + reproduction, and activity of organisms, including fungal cells; decreases the + number of fungi or pests present; deters microbial growth and degradation of + other ingredients in the formulation. Indicate the biocide used on the location + where the sample was taken. Multiple terms can be separated by pipes + title: biocide examples: - - value: obligate - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - slot_uri: MIXS:0001315 - multivalued: false - range: HOST_DEPENDENCE_ENUM - required: true - host_diet: - name: host_diet - description: Type of diet depending on the host, for animals omnivore, herbivore - etc., for humans high-fat, meditteranean etc.; can include multiple diet types - title: host diet + - value: Quaternary ammonium compound|SterBac from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - diet - - host - - host. - slot_uri: MIXS:0000869 + string_serialization: '{text}' + slot_uri: MIXS:0001258 multivalued: true - range: string required: false recommended: false - host_disease_stat: - name: host_disease_stat + biol_stat: + name: biol_stat annotations: Expected_value: tag: Expected_value - value: disease name or Disease Ontology term - description: List of diseases with which the host has been diagnosed; can include - multiple diagnoses. The value of the field depends on host; for humans the terms - should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, - non-human host diseases are free text - title: host disease status - in_subset: - - nucleic acid sequence source + value: enumeration + description: The level of genome modification + title: biological status + examples: + - value: natural from_schema: https://w3id.org/mixs-6-2-rc keywords: - - disease - - host - - host. - status - string_serialization: '{termLabel} [{termID}]|{text}' - slot_uri: MIXS:0000031 + string_serialization: '[wild|natural|semi-natural|inbred line|breeder''s line|hybrid|clonal + selection|mutant]' + slot_uri: MIXS:0000858 multivalued: false - host_dry_mass: - name: host_dry_mass + required: false + recommended: false + biomass: + name: biomass annotations: + Expected_value: + tag: Expected_value + value: biomass type;measurement value Preferred_unit: tag: Preferred_unit - value: kilogram, gram - description: Measurement of dry mass - title: host dry mass + value: ton, kilogram, gram + description: Amount of biomass; should include the name for the part of biomass + measured, e.g. Microbial, total. Can include multiple measurements + title: biomass examples: - - value: 500 gram + - value: total;20 gram from_schema: https://w3id.org/mixs-6-2-rc keywords: - - dry - - host - - host. - - mass - slot_uri: MIXS:0000257 - multivalued: false - range: string + - biomass + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000174 + multivalued: true required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - host_fam_rel: - name: host_fam_rel - annotations: - Expected_value: - tag: Expected_value - value: relationship type;arbitrary identifier - description: Relationships to other hosts in the same study; can include multiple - relationships - title: host family relationship + biotic_regm: + name: biotic_regm + description: Information about treatment(s) involving use of biotic factors, such + as bacteria, viruses or fungi + title: biotic regimen + examples: + - value: sample inoculated with Rhizobium spp. Culture from_schema: https://w3id.org/mixs-6-2-rc keywords: - - family - - host - - host. - - relationship - string_serialization: '{text};{text}' - slot_uri: MIXS:0000872 + - regimen + slot_uri: MIXS:0001038 multivalued: true - required: false - recommended: false - host_genotype: - name: host_genotype - description: Observed genotype - title: host genotype + range: string + biotic_relationship: + name: biotic_relationship + description: Description of relationship(s) between the subject organism and other + organism(s) it is associated with. E.g., parasite on species X; mutualist with + species Y. The target organism is the subject of the relationship, and the other + organism(s) is the object + title: observed biotic relationship + examples: + - value: free living + in_subset: + - nucleic acid sequence source from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - slot_uri: MIXS:0000365 + - observed + - relationship + slot_uri: MIXS:0000028 multivalued: false - range: string - host_growth_cond: - name: host_growth_cond - description: Literature reference giving growth conditions of the host - title: host growth conditions + range: BIOTIC_RELATIONSHIP_ENUM + birth_control: + name: birth_control + annotations: + Expected_value: + tag: Expected_value + value: medication name + description: Specification of birth control medication used + title: birth control + from_schema: https://w3id.org/mixs-6-2-rc + string_serialization: '{text}' + slot_uri: MIXS:0000286 + multivalued: false + required: false + recommended: false + bishomohopanol: + name: bishomohopanol + annotations: + Preferred_unit: + tag: Preferred_unit + value: microgram per liter, microgram per gram + description: Concentration of bishomohopanol + title: bishomohopanol examples: - - value: https://academic.oup.com/icesjms/article/68/2/349/617247 + - value: 14 microgram per liter from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - condition - - growth - - host - - host. - slot_uri: MIXS:0000871 + slot_uri: MIXS:0000175 multivalued: false range: string required: false recommended: false - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}|{text}$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - host_height: - name: host_height + blood_blood_disord: + name: blood_blood_disord + description: History of blood disorders; can include multiple disorders. The + terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + hematopoietic system disease (https://disease-ontology.org/?id=DOID:74) + title: blood/blood disorder + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - disorder + slot_uri: MIXS:0000271 + multivalued: true + range: string + required: false + recommended: false + blood_press_diast: + name: blood_press_diast annotations: Preferred_unit: tag: Preferred_unit - value: centimeter, millimeter, meter - description: The height of subject - title: host height + value: millimeter mercury + description: Resting diastolic blood pressure, measured as mm mercury + title: host blood pressure diastolic from_schema: https://w3id.org/mixs-6-2-rc keywords: - - height - host - host. - slot_uri: MIXS:0000264 + - pressure + slot_uri: MIXS:0000258 multivalued: false range: string + required: false + recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - host_hiv_stat: - name: host_hiv_stat + blood_press_syst: + name: blood_press_syst annotations: - Expected_value: - tag: Expected_value - value: HIV status;HAART initiation status - description: HIV status of subject, if yes HAART initiation status should also - be indicated as [YES or NO] - title: host HIV status - examples: - - value: yes;yes + Preferred_unit: + tag: Preferred_unit + value: millimeter mercury + description: Resting systolic blood pressure, measured as mm mercury + title: host blood pressure systolic from_schema: https://w3id.org/mixs-6-2-rc keywords: - host - host. - - status - string_serialization: '{boolean};{boolean}' - slot_uri: MIXS:0000265 + - pressure + slot_uri: MIXS:0000259 multivalued: false + range: string required: false recommended: false - host_infra_spec_name: - name: host_infra_spec_name - description: Taxonomic information about the host below subspecies level - title: host infra-specific name + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + bromide: + name: bromide + annotations: + Preferred_unit: + tag: Preferred_unit + value: parts per million + description: Concentration of bromide + title: bromide + examples: + - value: 0.05 parts per million from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - slot_uri: MIXS:0000253 + slot_uri: MIXS:0000176 multivalued: false range: string required: false recommended: false - host_infra_spec_rank: - name: host_infra_spec_rank - description: Taxonomic rank information about the host below subspecies level, - such as variety, form, rank etc - title: host infra-specific rank + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + build_docs: + name: build_docs + description: The building design, construction and operation documents + title: design, construction, and operation documents + examples: + - value: maintenance plans from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - - rank - slot_uri: MIXS:0000254 + - documents + slot_uri: MIXS:0000787 multivalued: false - range: string + range: BUILD_DOCS_ENUM required: false recommended: false - host_last_meal: - name: host_last_meal - annotations: - Expected_value: - tag: Expected_value - value: content;duration - description: Content of last meal and time since feeding; can include multiple - values - title: host last meal + build_occup_type: + name: build_occup_type + description: The primary function for which a building or discrete part of a building + is intended to be used + title: building occupancy type + examples: + - value: market from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - string_serialization: '{text};{duration}' - slot_uri: MIXS:0000870 + - type + slot_uri: MIXS:0000761 multivalued: true - required: false - recommended: false - host_length: - name: host_length + range: BUILD_OCCUP_TYPE_ENUM + required: true + building_setting: + name: building_setting + description: A location (geography) where a building is set + title: building setting + examples: + - value: rural + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000768 + multivalued: false + range: BUILDING_SETTING_ENUM + required: true + built_struc_age: + name: built_struc_age annotations: Preferred_unit: tag: Preferred_unit - value: centimeter, millimeter, meter - description: The length of subject - title: host length + value: year + description: The age of the built structure since construction + title: built structure age examples: - - value: 1 meter + - value: 15 years from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - - length - slot_uri: MIXS:0000256 + - age + slot_uri: MIXS:0000145 multivalued: false range: string + required: false + recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - host_life_stage: - name: host_life_stage - annotations: - Expected_value: - tag: Expected_value - value: stage - description: Description of life stage of host - title: host life stage - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - life - string_serialization: '{text}' - slot_uri: MIXS:0000251 - multivalued: false - host_number: - name: host_number - annotations: - Expected_value: - tag: Expected_value - value: count - description: Number of symbiotic host individuals pooled at the time of collection - title: host number individual + built_struc_set: + name: built_struc_set + description: The characterization of the location of the built structure as high + or low human density + title: built structure setting examples: - - value: '3' + - value: rural from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - number - string_serialization: '{float} m' - slot_uri: MIXS:0001305 + slot_uri: MIXS:0000778 multivalued: false + range: BUILT_STRUC_SET_ENUM required: false recommended: false - host_occupation: - name: host_occupation - description: Most frequent job performed by subject - title: host occupation - comments: - - Couldn't convert host_occupation with value veterinary to integer - - almost all host_occupation values in the NCBI biosample_set are strings, not - integers - examples: - - value: veterinary + built_struc_type: + name: built_struc_type + description: A physical structure that is a body or assemblage of bodies in space + to form a system capable of supporting loads + title: built structure type from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - slot_uri: MIXS:0000896 + - type + slot_uri: MIXS:0000721 + multivalued: false range: string required: false recommended: false - host_of_host_coinf: - name: host_of_host_coinf + calcium: + name: calcium annotations: - Expected_value: - tag: Expected_value - value: species name of coinfecting organism(s) - description: The taxonomic name of any coinfecting organism observed in a symbiotic - relationship with the host of the sampled host organism. e.g. where a sample - collected from a host trematode species (A) which was collected from a host_of_host - fish (B) that was also infected with a nematode (C), the value here would be - (C) the nematode {species name} or {common name}. Multiple co-infecting species - may be added in a comma-separated list. For listing symbiotic organisms associated - with the host (A) use the term Observed host symbiont - title: observed coinfecting organisms in host of host + Preferred_unit: + tag: Preferred_unit + value: milligram per liter, micromole per liter, parts per million + description: Concentration of calcium in the sample + title: calcium examples: - - value: Maritrema novaezealandense + - value: 0.2 micromole per liter from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - observed - - organism - string_serialization: '{text}' - slot_uri: MIXS:0001310 + slot_uri: MIXS:0000432 multivalued: false + range: string required: false recommended: false - host_of_host_disease: - name: host_of_host_disease + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + carb_dioxide: + name: carb_dioxide annotations: - Expected_value: - tag: Expected_value - value: disease name or Disease Ontology term - description: List of diseases with which the host of the symbiotic host organism - has been diagnosed; can include multiple diagnoses. The value of the field depends - on host; for humans the terms should be chosen from the DO (Human Disease Ontology) - at https://www.disease-ontology.org, non-human host diseases are free text - title: host of the symbiotic host disease status + Preferred_unit: + tag: Preferred_unit + value: micromole per liter, parts per million + description: Carbon dioxide (gas) amount or concentration at the time of sampling + title: carbon dioxide examples: - - value: rabies [DOID:11260] + - value: 410 parts per million from_schema: https://w3id.org/mixs-6-2-rc keywords: - - disease - - host - - host. - - status - - symbiosis - string_serialization: '{termLabel} [{termID}]|{text}' - slot_uri: MIXS:0001319 - multivalued: true - required: false - recommended: false - host_of_host_env_loc: - name: host_of_host_env_loc + - carbon + slot_uri: MIXS:0000097 + multivalued: false + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + carb_monoxide: + name: carb_monoxide annotations: - Expected_value: - tag: Expected_value - value: UBERON term(s), multiple values can be separated by pipes - description: For a symbiotic host organism the local anatomical environment within - its host may have causal influences. Report the anatomical entity(s) which are - in the direct environment of the symbiotic host organism being sampled and which - you believe have significant causal influences on your sample or specimen. For - example, if the symbiotic host organism being sampled is an intestinal worm, - its local environmental context will be the term for intestine from UBERON (http://uberon.github.io/) - title: host of the symbiotic host local environmental context + Preferred_unit: + tag: Preferred_unit + value: micromole per liter, parts per million + description: Carbon monoxide (gas) amount or concentration at the time of sampling + title: carbon monoxide examples: - - value: small intestine[uberon:0002108] + - value: 0.1 parts per million from_schema: https://w3id.org/mixs-6-2-rc keywords: - - context - - environmental - - host - - host. - - symbiosis - string_serialization: small intestine [UBERON:0002108] - slot_uri: MIXS:0001325 - multivalued: true + - carbon + slot_uri: MIXS:0000098 + multivalued: false + range: string required: false recommended: false - host_of_host_env_med: - name: host_of_host_env_med + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + carb_nitro_ratio: + name: carb_nitro_ratio annotations: Expected_value: tag: Expected_value - value: An ontology term for a material such as a tissue type or excreted substance - description: 'Report the environmental material(s) immediately surrounding the - symbiotic host organism at the time of sampling. This usually will be a tissue - or substance type from the host, but may be another material if the symbiont - is external to the host. We recommend using classes from the UBERON ontology, - but subclasses of ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483) - may also be used. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS - . Terms from other OBO ontologies are permissible as long as they reference - mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities - (e.g. intestines, heart).MIxS . Terms from other OBO ontologies are permissible - as long as they reference mass/volume nouns (e.g. air, water, blood) and not - discrete, countable entities (e.g. intestines, heart)' - title: host of the symbiotic host environemental medium + value: measurement value + description: Ratio of amount or concentrations of carbon to nitrogen + title: carbon/nitrogen ratio examples: - - value: feces[uberon:0001988] + - value: '0.417361111' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - environmental - - host - - host. - - symbiosis - string_serialization: '{termLabel} [{termID}]' - slot_uri: MIXS:0001326 + - carbon + - nitrogen + - ratio + string_serialization: '{float}:{float}' + slot_uri: MIXS:0000310 + range: float required: false recommended: false - host_of_host_fam_rel: - name: host_of_host_fam_rel + ceil_area: + name: ceil_area annotations: - Expected_value: - tag: Expected_value - value: relationship type;arbitrary identifier - description: Familial relationship of the host of the symbiotic host organisms - to other hosts of symbiotic host organism in the same study; can include multiple - relationships - title: host of the symbiotic host family relationship - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - family - - host - - host. - - relationship - - symbiosis - string_serialization: '{text};{text}' - slot_uri: MIXS:0001328 - multivalued: true - required: false - recommended: false - host_of_host_geno: - name: host_of_host_geno - description: Observed genotype of the host of the symbiotic host organism - title: host of the symbiotic host genotype + Preferred_unit: + tag: Preferred_unit + value: square meter + description: The area of the ceiling space within the room + title: ceiling area + examples: + - value: 25 square meter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - - symbiosis - slot_uri: MIXS:0001331 + - area + - ceiling + slot_uri: MIXS:0000148 multivalued: false range: string required: false recommended: false - host_of_host_gravid: - name: host_of_host_gravid - annotations: - Expected_value: - tag: Expected_value - value: gravidity status;timestamp - description: Whether or not the host of the symbiotic host organism is gravid, - and if yes date due or date post-conception, specifying which is used - title: host of the symbiotic host gravidity + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + ceil_cond: + name: ceil_cond + description: The physical condition of the ceiling at the time of sampling; photos + or video preferred; use drawings to indicate location of damaged areas + title: ceiling condition + examples: + - value: damaged from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - - symbiosis - string_serialization: '{boolean};{timestamp}' - slot_uri: MIXS:0001333 + - ceiling + - condition + slot_uri: MIXS:0000779 multivalued: false + range: SHARED_ENUM_3 required: false recommended: false - host_of_host_infname: - name: host_of_host_infname - description: Taxonomic name information of the host of the symbiotic host organism - below subspecies level - title: host of the symbiotic host infra-specific name - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - symbiosis - slot_uri: MIXS:0001329 - multivalued: false - range: string - required: false - recommended: false - host_of_host_infrank: - name: host_of_host_infrank - description: Taxonomic rank information about the host of the symbiotic host organism - below subspecies level, such as variety, form, rank etc - title: host of the symbiotic host infra-specific rank - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - rank - - symbiosis - slot_uri: MIXS:0001330 - multivalued: false - range: string - required: false - recommended: false - host_of_host_name: - name: host_of_host_name - description: Common name of the host of the symbiotic host organism - title: host of the symbiotic host common name + ceil_finish_mat: + name: ceil_finish_mat + description: The type of material used to finish a ceiling + title: ceiling finish material examples: - - value: snail - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - symbiosis - slot_uri: MIXS:0001324 - range: string - required: false - recommended: false - host_of_host_pheno: - name: host_of_host_pheno - annotations: - Expected_value: - tag: Expected_value - value: phenotype of the host of the symbiotic organism; PATO - description: Phenotype of the host of the symbiotic host organism. For phenotypic - quality ontology (PATO) terms, see http://purl.bioontology.org/ontology/pato - title: host of the symbiotic host phenotype + - value: stucco from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - - symbiosis - string_serialization: '{term}' - slot_uri: MIXS:0001332 + - ceiling + - material + slot_uri: MIXS:0000780 multivalued: false + range: CEIL_FINISH_MAT_ENUM required: false recommended: false - host_of_host_sub_id: - name: host_of_host_sub_id - description: 'A unique identifier by which each host of the symbiotic host organism - subject can be referred to, de-identified, e.g. #H14' - title: host of the symbiotic host subject id + ceil_struc: + name: ceil_struc + description: The construction format of the ceiling + title: ceiling structure examples: - - value: H3 + - value: concrete from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - - identifier - - symbiosis - slot_uri: MIXS:0001327 + - ceiling + slot_uri: MIXS:0000782 multivalued: false - range: string + range: CEIL_STRUC_ENUM required: false recommended: false - host_of_host_taxid: - name: host_of_host_taxid - annotations: - Expected_value: - tag: Expected_value - value: NCBI taxon identifier of the host of the symbiotic taxon organism - description: NCBI taxon id of the host of the symbiotic host organism - title: host of the symbiotic host taxon id + ceil_texture: + name: ceil_texture + description: The feel, appearance, or consistency of a ceiling surface + title: ceiling texture examples: - - value: '145637' + - value: popcorn from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - - identifier - - symbiosis - - taxon - string_serialization: '{integer}' - slot_uri: MIXS:0001306 + - ceiling + - texture + slot_uri: MIXS:0000783 multivalued: false + range: SHARED_ENUM_4 required: false recommended: false - host_of_host_totmass: - name: host_of_host_totmass - description: Total mass of the host of the symbiotic host organism at collection, - the unit depends on the host - title: host of the symbiotic host total mass + ceil_thermal_mass: + name: ceil_thermal_mass + annotations: + Preferred_unit: + tag: Preferred_unit + value: joule per degree Celsius + description: The ability of the ceiling to provide inertia against temperature + fluctuations. Generally this means concrete that is exposed. A metal deck that + supports a concrete slab will act thermally as long as it is exposed to room + air flow + title: ceiling thermal mass from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. + - ceiling - mass - - symbiosis - - total - slot_uri: MIXS:0001334 + slot_uri: MIXS:0000143 multivalued: false range: string required: false @@ -9293,71 +7578,90 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - host_phenotype: - name: host_phenotype - annotations: - Expected_value: - tag: Expected_value - value: PATO or HP - description: Phenotype of human or other host. Use terms from the phenotypic quality - ontology (pato) or the Human Phenotype Ontology (HP) - title: host phenotype + ceil_type: + name: ceil_type + description: The type of ceiling according to the ceiling's appearance or construction + title: ceiling type + examples: + - value: coffered from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - string_serialization: '{termLabel} [{termID}]' - slot_uri: MIXS:0000874 + - ceiling + - type + slot_uri: MIXS:0000784 multivalued: false - host_pred_appr: - name: host_pred_appr - description: Tool or approach used for host prediction - title: host prediction approach + range: CEIL_TYPE_ENUM + required: false + recommended: false + ceil_water_mold: + name: ceil_water_mold + description: Signs of the presence of mold or mildew on the ceiling + title: ceiling signs of water/mold examples: - - value: CRISPR spacer match - in_subset: - - sequencing + - value: presence of mold visible from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - - predict - slot_uri: MIXS:0000088 + - ceiling + slot_uri: MIXS:0000781 multivalued: false - range: HOST_PRED_APPR_ENUM - host_pred_est_acc: - name: host_pred_est_acc - description: For each tool or approach used for host prediction, estimated false - discovery rates should be included, either computed de novo or from the literature - title: host prediction estimated accuracy + range: SHARED_ENUM_1 + required: false + recommended: false + chem_administration: + name: chem_administration + annotations: + Expected_value: + tag: Expected_value + value: CHEBI;timestamp + description: List of chemical compounds administered to the host or site where + sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can + include multiple compounds. For chemical entities of biological interest ontology + (chebi) (v 163), http://purl.bioontology.org/ontology/chebi + title: chemical administration examples: - - value: 'CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host - genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048)' - in_subset: - - sequencing + - value: agar [CHEBI:2509];2018-05-11T20:00Z from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - - predict - slot_uri: MIXS:0000089 - multivalued: false - range: string - host_pulse: - name: host_pulse + - administration + string_serialization: '{termLabel} [{termID}];{timestamp}' + slot_uri: MIXS:0000751 + multivalued: true + chem_mutagen: + name: chem_mutagen annotations: + Expected_value: + tag: Expected_value + value: mutagen name;mutagen amount;treatment interval and duration Preferred_unit: tag: Preferred_unit - value: beats per minute - description: Resting pulse, measured as beats per minute - title: host pulse + value: milligram per liter + description: Treatment involving use of mutagens; should include the name of mutagen, + amount administered, treatment regimen including how many times the treatment + was repeated, how long each treatment lasted, and the start and end time of + the entire treatment; can include multiple mutagen regimens + title: chemical mutagen examples: - - value: 65 beats per minute + - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + from_schema: https://w3id.org/mixs-6-2-rc + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000555 + multivalued: true + required: false + recommended: false + chem_oxygen_dem: + name: chem_oxygen_dem + annotations: + Preferred_unit: + tag: Preferred_unit + value: milligram per liter + description: A measure of the capacity of water to consume oxygen during the decomposition + of organic matter and the oxidation of inorganic chemicals such as ammonia and + nitrite + title: chemical oxygen demand from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - slot_uri: MIXS:0000333 + - oxygen + slot_uri: MIXS:0000656 multivalued: false range: string required: false @@ -9368,210 +7672,105 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - host_sex: - name: host_sex + chem_treat_method: + name: chem_treat_method annotations: Expected_value: tag: Expected_value - value: enumeration - description: Gender or physical sex of the host - title: host sex - comments: - - example of non-binary from Excel sheets does not match any of the enumerated - values - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - string_serialization: '[female|hermaphrodite|non-binary|male|transgender|transgender - (female to male)|transgender (male to female) - - |undeclared]' - slot_uri: MIXS:0000811 - required: false - recommended: false - host_shape: - name: host_shape - description: Morphological shape of host - title: host shape - examples: - - value: round + value: measurement value;frequency;duration;duration + Preferred_unit: + tag: Preferred_unit + value: milligram per liter + description: Method of chemical administration(dose, frequency, duration, time + elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 + hr; 0 days) + title: chemical treatment method from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - slot_uri: MIXS:0000261 + - method + - treatment + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}' + slot_uri: MIXS:0000457 multivalued: false - range: string required: false recommended: false - host_spec_range: - name: host_spec_range + chem_treatment: + name: chem_treatment annotations: Expected_value: tag: Expected_value - value: NCBI taxid - description: The range and diversity of host species that an organism is capable - of infecting, defined by NCBI taxonomy identifier - title: host specificity or range - examples: - - value: '9606' - in_subset: - - nucleic acid sequence source - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - range - string_serialization: '{integer}' - slot_uri: MIXS:0000030 - multivalued: true - host_specificity: - name: host_specificity - description: 'Level of specificity of symbiont-host interaction: e.g. generalist - (symbiont able to establish associations with distantly related hosts) or species-specific' - title: host specificity + value: name;name;timestamp + description: List of chemical compounds administered upstream the sampling location + where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, + demulsifiers, and other production chemicals etc.). The commercial name of the + product and name of the supplier should be provided. The date of administration + should also be included + title: chemical treatment examples: - - value: species-specific - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - slot_uri: MIXS:0001308 - multivalued: false - range: HOST_SPECIFICITY_ENUM - recommended: true - host_subject_id: - name: host_subject_id - description: A unique identifier by which each subject can be referred to, de-identified - title: host subject id + - value: ACCENT 1125;DOW;2010-11-17 from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - - identifier - slot_uri: MIXS:0000861 + - treatment + string_serialization: '{text};{text};{timestamp}' + slot_uri: MIXS:0001012 multivalued: false - range: string - required: false - recommended: false - host_subspecf_genlin: - name: host_subspecf_genlin - annotations: - Expected_value: - tag: Expected_value - value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, - e.g. serovar, biotype, ecotype, variety, cultivar - description: Information about the genetic distinctness of the host organism below - the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, - or any relevant genetic typing schemes like Group I plasmid. Subspecies should - not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage - name and the lineage rank separated by a colon, e.g., biovar:abc123 - title: host subspecific genetic lineage - examples: - - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious' - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - lineage - string_serialization: '{rank name}:{text}' - slot_uri: MIXS:0001318 - multivalued: true required: false recommended: false - host_substrate: - name: host_substrate - description: The growth substrate of the host - title: host substrate + chimera_check: + name: chimera_check + description: Tool(s) used for chimera checking, including version number and parameters, + to discover and remove chimeric sequences. A chimeric sequence is comprised + of two or more phylogenetically distinct parent sequences + title: chimera check software examples: - - value: rock + - value: uchime;v4.1;default parameters + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - slot_uri: MIXS:0000252 + - software + slot_uri: MIXS:0000052 multivalued: false range: string - required: false - recommended: false - host_symbiont: - name: host_symbiont - annotations: - Expected_value: - tag: Expected_value - value: species name or common name - description: The taxonomic name of the organism(s) found living in mutualistic, - commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont - can have its own symbionts. For example, parasites may have hyperparasites (=parasites - of the parasite) - title: observed host symbionts - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - observed - - symbiosis - string_serialization: '{text}' - slot_uri: MIXS:0001298 - multivalued: true - required: false - recommended: false - host_taxid: - name: host_taxid - annotations: - Expected_value: - tag: Expected_value - value: NCBI taxon identifier - description: NCBI taxon id of the host, e.g. 9606 - title: host taxid - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - taxon - slot_uri: MIXS:0000250 - multivalued: false - host_tot_mass: - name: host_tot_mass + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{software};{version};{parameters}$ + interpolated: true + partial_match: true + chloride: + name: chloride annotations: Preferred_unit: tag: Preferred_unit - value: kilogram, gram - description: Total mass of the host at collection, the unit depends on host - title: host total mass + value: milligram per liter, parts per million + description: Concentration of chloride in the sample + title: chloride + examples: + - value: 5000 milligram per liter from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - mass - - total - slot_uri: MIXS:0000263 + slot_uri: MIXS:0000429 multivalued: false range: string + required: false + recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - host_wet_mass: - name: host_wet_mass + chlorophyll: + name: chlorophyll annotations: Preferred_unit: tag: Preferred_unit - value: kilogram, gram - description: Measurement of wet mass - title: host wet mass + value: milligram per cubic meter, microgram per liter + description: Concentration of chlorophyll + title: chlorophyll examples: - - value: 1500 gram + - value: 5 milligram per cubic meter from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - mass - - wet - slot_uri: MIXS:0000567 + slot_uri: MIXS:0000177 multivalued: false range: string required: false @@ -9582,151 +7781,135 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - hrt: - name: hrt - description: Whether subject had hormone replacement theraphy, and if yes start - date - title: HRT + climate_environment: + name: climate_environment + description: Treatment involving an exposure to a particular climate; treatment + regimen including how many times the treatment was repeated, how long each treatment + lasted, and the start and end time of the entire treatment; can include multiple + climates + title: climate environment examples: - - value: '2013-03-25T12:42:31+01:00' - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000969 - multivalued: false - range: datetime - required: false - recommended: false - humidity: - name: humidity - description: Amount of water vapour in the air, at the time of sampling - title: humidity + - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc keywords: - - humidity - slot_uri: MIXS:0000100 - multivalued: false + - environment + slot_uri: MIXS:0001040 + multivalued: true range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - humidity_regm: - name: humidity_regm + coll_site_geo_feat: + name: coll_site_geo_feat annotations: Expected_value: tag: Expected_value - value: humidity value;treatment interval and duration - Preferred_unit: - tag: Preferred_unit - value: gram per cubic meter - description: Information about treatment involving an exposure to varying degree - of humidity; information about treatment involving use of growth hormones; should - include amount of humidity administered, treatment regimen including how many - times the treatment was repeated, how long each treatment lasted, and the start - and end time of the entire treatment; can include multiple regimens - title: humidity regimen - examples: - - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - humidity - - regimen - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000568 - multivalued: true - required: false - recommended: false - hygienic_area: - name: hygienic_area - annotations: - Expected_value: - tag: Expected_value - value: Expected value - description: The subdivision of areas within a food production facility according - to hygienic requirements. This field accepts terms listed under hygienic food - production area (http://purl.obolibrary.org/obo/ENVO). Please add a term that - most accurately indicates the hygienic area your sample was taken from according - to the definitions provided - title: hygienic food production area + value: ENVO:00000002 or ENVO:00000070 + description: 'Text or terms that describe the geographic feature where the food + sample was obtained by the researcher. This field accepts selected terms listed + under the following ontologies: anthropogenic geographic feature (http://purl.obolibrary.org/obo/ENVO_00000002), + for example agricultural fairground [ENVO:01000986]; garden [ENVO:00000011} + or any of its subclasses; market [ENVO:01000987]; water well [ENVO:01000002]; + or human construction (http://purl.obolibrary.org/obo/ENVO_00000070)' + title: collection site geographic feature examples: - - value: Low Hygiene Area + - value: farm [ENVO:00000078] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - area - - food - - production - string_serialization: '{text}' - slot_uri: MIXS:0001253 + - feature + - geographic + - site + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001183 multivalued: false - required: false - recommended: false - hysterectomy: - name: hysterectomy - description: Specification of whether hysterectomy was performed - title: hysterectomy + required: true + collection_date: + name: collection_date + description: 'The time of sampling, either as an instance (single point in time) + or interval. In case no exact time is available, the date/time can be right + truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; + 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant' + title: collection date examples: - - value: 'no' + - value: '2013-03-25T12:42:31+01:00' + in_subset: + - environment from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000287 + keywords: + - date + slot_uri: MIXS:0000011 multivalued: false - range: boolean - required: false - recommended: false - ihmc_medication_code: - name: ihmc_medication_code - description: Can include multiple medication codes - title: IHMC medication code + range: datetime + required: true + compl_appr: + name: compl_appr + annotations: + Expected_value: + tag: Expected_value + value: text + description: The approach used to determine the completeness of a given genomic + assembly, which would typically make use of a set of conserved marker genes + or a closely related reference genome. For UViG completeness, include reference + genome or group used, and contig feature suggesting a complete genome + title: completeness approach examples: - - value: '810' + - value: other + description: was other UViG length compared to the average length of + reference genomes from the P22virus genus (NCBI RefSeq v83) + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - code - slot_uri: MIXS:0000884 - multivalued: true - range: integer - required: false - recommended: false - indoor_space: - name: indoor_space - description: A distinguishable space within a structure, the purpose for which - discrete areas of a building is used - title: indoor space + slot_uri: MIXS:0000071 + range: COMPL_APPR_ENUM + compl_score: + name: compl_score + annotations: + Expected_value: + tag: Expected_value + value: quality;percent completeness + description: 'Completeness score is typically based on either the fraction of + markers found as compared to a database or the percent of a genome found as + compared to a closely related reference genome. High Quality Draft: >90%, Medium + Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated + completeness scores' + title: completeness score examples: - - value: foyer + - value: med;60% + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - indoor - slot_uri: MIXS:0000763 + - score + string_serialization: '[high|med|low];{percentage}' + slot_uri: MIXS:0000069 multivalued: false - range: INDOOR_SPACE_ENUM - required: true - indoor_surf: - name: indoor_surf - description: Type of indoor surface - title: indoor surface + compl_software: + name: compl_software + annotations: + Expected_value: + tag: Expected_value + value: names and versions of software(s) used + description: Tools used for completion estimate, i.e. checkm, anvi'o, busco + title: completeness software examples: - - value: wall + - value: checkm + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - indoor - - surface - slot_uri: MIXS:0000764 + - software + string_serialization: '{software};{version}' + slot_uri: MIXS:0000070 multivalued: false - range: INDOOR_SURF_ENUM - indust_eff_percent: - name: indust_eff_percent + conduc: + name: conduc annotations: Preferred_unit: tag: Preferred_unit - value: percentage - description: Percentage of industrial effluents received by wastewater treatment - plant - title: industrial effluent percent + value: milliSiemens per centimeter + description: Electrical conductivity of water + title: conductivity + examples: + - value: 10 milliSiemens per centimeter from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - percent - slot_uri: MIXS:0000662 + slot_uri: MIXS:0000692 multivalued: false range: string required: false @@ -9737,322 +7920,187 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - inorg_particles: - name: inorg_particles - annotations: - Expected_value: - tag: Expected_value - value: inorganic particle name;measurement value - Preferred_unit: - tag: Preferred_unit - value: mole per liter, milligram per liter - description: Concentration of particles such as sand, grit, metal particles, ceramics, - etc.; can include multiple particles - title: inorganic particles - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - inorganic - - particle - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000664 - multivalued: true - required: false - recommended: false - inside_lux: - name: inside_lux + cons_food_stor_dur: + name: cons_food_stor_dur annotations: Preferred_unit: tag: Preferred_unit - value: kilowatt per square metre - description: The recorded value at sampling time (power density) - title: inside lux light + value: hours or days + description: The storage duration of the food commodity by the consumer, prior + to onset of illness or sample collection. Indicate the timepoint written in + ISO 8601 format + title: food stored by consumer (storage duration) + examples: + - value: P5D from_schema: https://w3id.org/mixs-6-2-rc keywords: - - inside - - light - slot_uri: MIXS:0000168 + - consumer + - duration) + - food + - storage + slot_uri: MIXS:0001195 multivalued: false range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: ^{duration}$ interpolated: true partial_match: true - int_wall_cond: - name: int_wall_cond - description: The physical condition of the wall at the time of sampling; photos - or video preferred; use drawings to indicate location of damaged areas - title: interior wall condition + cons_food_stor_temp: + name: cons_food_stor_temp + annotations: + Expected_value: + tag: Expected_value + value: text or measurement value + Preferred_unit: + tag: Preferred_unit + value: degree Celsius + description: Temperature at which food commodity was stored by the consumer, prior + to onset of illness or sample collection + title: food stored by consumer (storage temperature) examples: - - value: damaged + - value: 4 degree Celsius from_schema: https://w3id.org/mixs-6-2-rc keywords: - - condition - - interior - - wall - slot_uri: MIXS:0000813 + - consumer + - food + - storage + - temperature + string_serialization: '{float} {unit}|{text}' + slot_uri: MIXS:0001196 multivalued: false - range: SHARED_ENUM_3 required: false recommended: false - intended_consumer: - name: intended_consumer - annotations: - Expected_value: - tag: Expected_value - value: FOODON_03510136 or NCBI taxid - description: Food consumer type, human or animal, for which the food product is - produced and marketed. This field accepts terms listed under food consumer group - (http://purl.obolibrary.org/obo/FOODON_03510136) or NCBI taxid - title: intended consumer - examples: - - value: 9606 o rsenior as food consumer [FOODON:03510254] - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - consumer - string_serialization: '{integer}|{termLabel} [{termID}]' - slot_uri: MIXS:0001144 - multivalued: true - isol_growth_condt: - name: isol_growth_condt - description: Publication reference in the form of pubmed ID (pmid), digital object - identifier (doi) or url for isolation and growth condition specifications of - the organism/material - title: isolation and growth condition - examples: - - value: doi:10.1016/j.syapm.2018.01.009 - in_subset: - - nucleic acid sequence source - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - condition - - growth - - isolation - slot_uri: MIXS:0000003 - multivalued: false - range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ - structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ - interpolated: true - partial_match: true - iw_bt_date_well: - name: iw_bt_date_well - description: Injection water breakthrough date per well following a secondary - and/or tertiary recovery - title: injection water breakthrough date of specific well + cons_purch_date: + name: cons_purch_date + description: The date a food product was purchased by consumer + title: purchase date examples: - value: '2013-03-25T12:42:31+01:00' from_schema: https://w3id.org/mixs-6-2-rc keywords: - date - - water - slot_uri: MIXS:0001010 + slot_uri: MIXS:0001197 multivalued: false range: datetime required: false recommended: false - iwf: - name: iwf - annotations: - Preferred_unit: - tag: Preferred_unit - value: percent - description: Proportion of the produced fluids derived from injected water at - the time of sampling. (e.g. 87%) - title: injection water fraction - comments: - - pattern was "[0-9]*\\.?[0-9]+ ?%" - - percent or float? - examples: - - value: '0.79' - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - fraction - - water - slot_uri: MIXS:0000455 - range: float - required: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - kidney_disord: - name: kidney_disord - description: History of kidney disorders; can include multiple disorders. The - terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - kidney disease (https://disease-ontology.org/?id=DOID:557) - title: urine/kidney disorder - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - disorder - slot_uri: MIXS:0000277 - multivalued: true - range: string - required: false - recommended: false - last_clean: - name: last_clean - description: The last time the floor was cleaned (swept, mopped, vacuumed) - title: last time swept/mopped/vacuumed + cons_qty_purchased: + name: cons_qty_purchased + description: The quantity of food purchased by consumer + title: quantity purchased examples: - - value: '2013-03-25T12:42:31+01:00' + - value: 5 cans from_schema: https://w3id.org/mixs-6-2-rc keywords: - - time - slot_uri: MIXS:0000814 + - quantity + slot_uri: MIXS:0001198 multivalued: false - range: datetime + range: string required: false recommended: false - lat_lon: - name: lat_lon - annotations: - Expected_value: - tag: Expected_value - value: decimal degrees, limit to 8 decimal points - description: The geographical origin of the sample as defined by latitude and - longitude. The values should be reported in decimal degrees and in WGS84 system - title: geographic location (latitude and longitude) - examples: - - value: 50.586825 6.408977 - in_subset: - - environment - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - geographic - - location - string_serialization: '{float} {float}' - slot_uri: MIXS:0000009 - required: true - pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$ + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{lat} {lon}$ + syntax: ^{integer} {text}$ interpolated: true partial_match: true - lib_layout: - name: lib_layout - description: Specify whether to expect single, paired, or other configuration - of reads - title: library layout + contam_score: + name: contam_score + description: 'The contamination score is based on the fraction of single-copy + genes that are observed more than once in a query genome. The following scores + are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low + Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be + deposited into any of the public databases' + title: contamination score examples: - - value: paired + - value: '0.01' in_subset: - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - library - slot_uri: MIXS:0000041 + - score + slot_uri: MIXS:0000072 multivalued: false - range: LIB_LAYOUT_ENUM - lib_reads_seqd: - name: lib_reads_seqd - description: Total number of clones sequenced from the library - title: library reads sequenced + range: float + contam_screen_input: + name: contam_screen_input + description: The type of sequence data used as input + title: contamination screening input examples: - - value: '20' + - value: contigs in_subset: - sequencing from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - library - slot_uri: MIXS:0000040 + slot_uri: MIXS:0000005 multivalued: false - range: integer - lib_screen: - name: lib_screen + range: CONTAM_SCREEN_INPUT_ENUM + contam_screen_param: + name: contam_screen_param annotations: Expected_value: tag: Expected_value - value: screening strategy name - description: Specific enrichment or screening methods applied before and/or after - creating libraries - title: library screening strategy + value: enumeration;value or name + description: Specific parameters used in the decontamination sofware, such as + reference database, coverage, and kmers. Combinations of these parameters may + also be used, i.e. kmer and coverage, or reference database and kmer + title: contamination screening parameters examples: - - value: enriched, screened, normalized + - value: kmer in_subset: - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - library - string_serialization: '{text}' - slot_uri: MIXS:0000043 + - parameter + string_serialization: '[ref db|kmer|coverage|combination];{text|integer}' + slot_uri: MIXS:0000073 multivalued: false - lib_size: - name: lib_size - description: Total number of clones in the library prepared for the project - title: library size + cool_syst_id: + name: cool_syst_id + description: The cooling system identifier + title: cooling system identifier examples: - - value: '50' - in_subset: - - sequencing + - value: '12345' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - library - - size - slot_uri: MIXS:0000039 + - identifier + slot_uri: MIXS:0000785 multivalued: false range: integer - lib_vector: - name: lib_vector + required: false + recommended: false + crop_rotation: + name: crop_rotation annotations: Expected_value: tag: Expected_value - value: vector - description: Cloning vector type(s) used in construction of libraries - title: library vector + value: crop rotation status;schedule + description: Whether or not crop is rotated, and if yes, rotation schedule + title: history/crop rotation examples: - - value: Bacteriophage P1 - in_subset: - - sequencing + - value: yes;R2/2017-01-01/2018-12-31/P6M from_schema: https://w3id.org/mixs-6-2-rc keywords: - - library - string_serialization: '{text}' - slot_uri: MIXS:0000042 + - history + slot_uri: MIXS:0000318 multivalued: false - library_prep_kit: - name: library_prep_kit + crop_yield: + name: crop_yield annotations: - Expected_value: - tag: Expected_value - value: name of library preparation kit - description: Packaged kits (containing adapters, indexes, enzymes, buffers etc.), - tailored for specific sequencing workflows, which allow the simplified preparation - of sequencing-ready libraries for small genomes, amplicons, and plasmids - title: library preparation kit + Preferred_unit: + tag: Preferred_unit + value: kilogram per metre square + description: Amount of crop produced per unit or area of land + title: crop yield + examples: + - value: 570 kilogram per metre square from_schema: https://w3id.org/mixs-6-2-rc keywords: - - kit - - library - - preparation - string_serialization: '{text}' - slot_uri: MIXS:0001145 + - crop + slot_uri: MIXS:0001116 multivalued: false - required: false - recommended: false - light_intensity: - name: light_intensity - annotations: - Preferred_unit: - tag: Preferred_unit - value: lux - description: Measurement of light intensity - title: light intensity - examples: - - value: 0.3 lux - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - intensity - - light - slot_uri: MIXS:0000706 - multivalued: false - range: string + range: string required: false recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? @@ -10061,150 +8109,157 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - light_regm: - name: light_regm - annotations: - Expected_value: - tag: Expected_value - value: exposure type;light intensity;light quality - Preferred_unit: - tag: Preferred_unit - value: lux; micrometer, nanometer, angstrom - description: Information about treatment(s) involving exposure to light, including - both light intensity and quality - title: light regimen + cult_isol_date: + name: cult_isol_date + description: The datetime marking the end of a process in which a sample yields + a positive result for the target microbial analyte(s) in the form of an isolated + colony or colonies + title: culture isolation date examples: - - value: incandescant light;10 lux;450 nanometer + - value: '2018-05-11T10:00:00+01:00' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - light - - regimen - string_serialization: '{text};{float} {unit};{float} {unit}' - slot_uri: MIXS:0000569 + - culture + - date + - isolation + slot_uri: MIXS:0001181 multivalued: false + range: datetime required: false recommended: false - light_type: - name: light_type - description: Application of light to achieve some practical or aesthetic effect. - Lighting includes the use of both artificial light sources such as lamps and - light fixtures, as well as natural illumination by capturing daylight. Can also - include absence of light - title: light type + cult_result: + name: cult_result + description: Any result of a bacterial culture experiment reported as a binary + assessment such as positive/negative, active/inactive + title: culture result examples: - - value: desk lamp + - value: positive from_schema: https://w3id.org/mixs-6-2-rc keywords: - - light - - type - slot_uri: MIXS:0000769 - multivalued: true - range: LIGHT_TYPE_ENUM - required: true - link_addit_analys: - name: link_addit_analys - description: Link to additional analysis results performed on the sample - title: links to additional analysis + - culture + slot_uri: MIXS:0001117 + multivalued: false + range: CULT_RESULT_ENUM + required: false + recommended: false + cult_result_org: + name: cult_result_org + description: Taxonomic information about the cultured organism(s) + title: culture result organism + examples: + - value: Listeria monocytogenes [NCIT:C86502] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - link - slot_uri: MIXS:0000340 - multivalued: false + - culture + - organism + slot_uri: MIXS:0001118 + multivalued: true range: string required: false recommended: false - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ + syntax: ^({termLabel} \[{termID}\])|{integer}$ interpolated: true partial_match: true - link_class_info: - name: link_class_info + cult_root_med: + name: cult_root_med annotations: Expected_value: tag: Expected_value - value: PMID,DOI or url - description: Link to digitized soil maps or other soil classification information - title: link to classification information + value: name, PMID,DOI or url + description: Name or reference for the hydroponic or in vitro culture rooting + medium; can be the name of a commonly used medium or reference to a specific + medium, e.g. Murashige and Skoog medium. If the medium has not been formally + published, use the rooting medium descriptors + title: culture rooting medium + examples: + - value: http://himedialabs.com/TD/PT158.pdf from_schema: https://w3id.org/mixs-6-2-rc keywords: - - classification - - information - - link - string_serialization: '{termLabel} [{termID}]' - slot_uri: MIXS:0000329 + - culture + string_serialization: '{text}|{PMID}|{DOI}|{URL}' + slot_uri: MIXS:0001041 multivalued: false required: false recommended: false - link_climate_info: - name: link_climate_info - description: Link to climate resource - title: link to climate information + cult_target: + name: cult_target + annotations: + Expected_value: + tag: Expected_value + value: NCIT:C14250 or NCBI taxid or culture independent + description: The target microbial analyte in terms of investigation scope. This + field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). + This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy + title: culture target microbial analyte + examples: + - value: Listeria monocytogenes [NCIT:C86502] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - information - - link - slot_uri: MIXS:0000328 - multivalued: false - range: string + - culture + - microbial + - target + string_serialization: '{termLabel} [{termID}]|{integer}' + slot_uri: MIXS:0001119 + multivalued: true required: false recommended: false - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ - structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ - interpolated: true - partial_match: true - lithology: - name: lithology - description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). - If "other" is specified, please propose entry in "additional info" field' - title: lithology + cur_land_use: + name: cur_land_use + annotations: + Expected_value: + tag: Expected_value + value: enumeration + description: Present state of sample site + title: current land use examples: - - value: Volcanic + - value: conifers from_schema: https://w3id.org/mixs-6-2-rc keywords: - - lithology - slot_uri: MIXS:0000990 + - land + - use + string_serialization: '[cities|farmstead|industrial areas|roads/railroads|rock|sand|gravel|mudflats|salt + flats|badlands|permanent snow or ice|saline seeps|mines/quarries|oil waste areas|small + grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands + (grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands + used for livestock grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub + land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)|successional + shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub + crops (blueberries,nursery ornamentals,filberts)|vine crops (grapes)|conifers + (e.g. pine,spruce,fir,cypress)|hardwoods (e.g. oak,hickory,elm,aspen)|intermixed + hardwood and conifers|tropical (e.g. mangrove,palms)|rainforest (evergreen forest + receiving >406 cm annual rainfall)|swamp (permanent or semi-permanent water + body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery + trees)]' + slot_uri: MIXS:0001080 multivalued: false - range: LITHOLOGY_ENUM - recommended: true - liver_disord: - name: liver_disord - description: History of liver disorders; can include multiple disorders. The terms - should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - liver disease (https://disease-ontology.org/?id=DOID:409) - title: liver disorder - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - disorder - slot_uri: MIXS:0000282 - multivalued: true - range: string required: false recommended: false - local_class: - name: local_class + cur_vegetation: + name: cur_vegetation annotations: Expected_value: tag: Expected_value - value: local classification name - description: Soil classification based on local soil classification system - title: soil_taxonomic/local classification + value: current vegetation type + description: Vegetation classification from one or more standard classification + systems, or agricultural crop + title: current vegetation from_schema: https://w3id.org/mixs-6-2-rc keywords: - - classification + - vegetation string_serialization: '{text}' - slot_uri: MIXS:0000330 + slot_uri: MIXS:0000312 multivalued: false - local_class_meth: - name: local_class_meth - description: Reference or method used in determining the local soil classification - title: soil_taxonomic/local classification method + cur_vegetation_meth: + name: cur_vegetation_meth + description: Reference or method used in vegetation classification + title: current vegetation method from_schema: https://w3id.org/mixs-6-2-rc keywords: - - classification - method - slot_uri: MIXS:0000331 + - vegetation + slot_uri: MIXS:0000314 multivalued: false range: string pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ @@ -10212,56 +8267,71 @@ slots: syntax: ^{PMID}|{DOI}|{URL}$ interpolated: true partial_match: true - lot_number: - name: lot_number - annotations: - Expected_value: - tag: Expected_value - value: lot number, item - description: 'A distinctive alpha-numeric identification code assigned by the - manufacturer or distributor to a specific quantity of manufactured material - or product within a batch. Synonym: Batch Number. The submitter should provide - lot number of the item followed by the item name for which the lot number was - provided' - title: lot number + date_extr_weath: + name: date_extr_weath + description: Date of unusual weather events that may have affected microbial populations. + Multiple terms can be separated by pipes, listed in reverse chronological order + title: extreme weather date examples: - - value: 1239ABC01A, split Cornish hens + - value: '2013-03-25T12:42:31+01:00' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - number - string_serialization: '{integer}, {text}' - slot_uri: MIXS:0001147 + - date + - extreme + - weather + slot_uri: MIXS:0001142 multivalued: true + range: datetime required: false recommended: false - mag_cov_software: - name: mag_cov_software - description: Tool(s) used to determine the genome coverage if coverage is used - as a binning parameter in the extraction of genomes from metagenomic datasets - title: MAG coverage software - examples: - - value: bbmap + date_last_rain: + name: date_last_rain + description: The date of the last time it rained + title: date last rain + examples: + - value: '2013-03-25T12:42:31+01:00' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - date + - rain + slot_uri: MIXS:0000786 + multivalued: false + range: datetime + required: false + recommended: false + decontam_software: + name: decontam_software + annotations: + Expected_value: + tag: Expected_value + value: enumeration + description: Tool(s) used in contamination screening + title: decontamination software + examples: + - value: anvi'o in_subset: - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - software - slot_uri: MIXS:0000080 + string_serialization: '[checkm/refinem|anvi''o|prodege|bbtools:decontaminate.sh|acdc|combination]' + slot_uri: MIXS:0000074 multivalued: false - range: MAG_COV_SOFTWARE_ENUM - magnesium: - name: magnesium + density: + name: density annotations: Preferred_unit: tag: Preferred_unit - value: mole per liter, milligram per liter, parts per million, micromole per - kilogram - description: Concentration of magnesium in the sample - title: magnesium + value: gram per cubic meter, gram per cubic centimeter + description: Density of the sample, which is its mass per unit volume (aka volumetric + mass density) + title: density examples: - - value: 52.8 micromole per kilogram + - value: 1000 kilogram per cubic meter from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000431 + keywords: + - density + slot_uri: MIXS:0000435 multivalued: false range: string required: false @@ -10272,76 +8342,87 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - maternal_health_stat: - name: maternal_health_stat - description: Specification of the maternal health status - title: amniotic fluid/maternal health status - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - status - slot_uri: MIXS:0000273 - multivalued: false - range: string - required: false - recommended: false - max_occup: - name: max_occup - description: The maximum amount of people allowed in the indoor environment - title: maximum occupancy + depos_env: + name: depos_env + description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). + If "other" is specified, please propose entry in "additional info" field + title: depositional environment from_schema: https://w3id.org/mixs-6-2-rc keywords: - - maximum - slot_uri: MIXS:0000229 + - environment + slot_uri: MIXS:0000992 multivalued: false - range: string - required: false - recommended: false - pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{integer} {text}$ - interpolated: true - partial_match: true - mean_frict_vel: - name: mean_frict_vel + range: DEPOS_ENV_ENUM + recommended: true + depth: + name: depth annotations: Preferred_unit: tag: Preferred_unit - value: meter per second - description: Measurement of mean friction velocity - title: mean friction velocity - examples: - - value: 0.5 meter per second + value: meter + description: The vertical distance below local surface. For sediment or soil samples + depth is measured from sediment or soil surface, respectively. Depth can be + reported as an interval for subsurface samples + title: depth + in_subset: + - environment from_schema: https://w3id.org/mixs-6-2-rc keywords: - - mean - - velocity - slot_uri: MIXS:0000498 + - depth + slot_uri: MIXS:0000018 multivalued: false range: string - required: false - recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - mean_peak_frict_vel: - name: mean_peak_frict_vel + dermatology_disord: + name: dermatology_disord + description: History of dermatology disorders; can include multiple disorders. + The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + skin disease (https://disease-ontology.org/?id=DOID:37) + title: dermatology disorder + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - disorder + slot_uri: MIXS:0000284 + multivalued: true + range: string + required: false + recommended: false + detec_type: + name: detec_type + annotations: + Expected_value: + tag: Expected_value + value: enumeration + description: Type of UViG detection + title: detection type + examples: + - value: independent sequence (UViG) + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - type + string_serialization: '[independent sequence (UViG)|provirus (UpViG)]' + slot_uri: MIXS:0000084 + multivalued: false + dew_point: + name: dew_point annotations: Preferred_unit: tag: Preferred_unit - value: meter per second - description: Measurement of mean peak friction velocity - title: mean peak friction velocity + value: degree Celsius + description: The temperature to which a given parcel of humid air must be cooled, + at constant barometric pressure, for water vapor to condense into water + title: dew point examples: - - value: 1 meter per second + - value: 22 degree Celsius from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - mean - - peak - - velocity - slot_uri: MIXS:0000502 + slot_uri: MIXS:0000129 multivalued: false range: string required: false @@ -10352,83 +8433,110 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - mech_struc: - name: mech_struc - description: 'mechanical structure: a moving structure' - title: mechanical structure + diet_last_six_month: + name: diet_last_six_month + annotations: + Expected_value: + tag: Expected_value + value: diet change;current diet + description: Specification of major diet changes in the last six months, if yes + the change should be specified + title: major diet change in last six months examples: - - value: elevator + - value: yes;vegetarian diet from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000815 + keywords: + - diet + - months + string_serialization: '{boolean};{text}' + slot_uri: MIXS:0000266 multivalued: false - range: MECH_STRUC_ENUM required: false recommended: false - mechanical_damage: - name: mechanical_damage + dietary_claim_use: + name: dietary_claim_use annotations: Expected_value: tag: Expected_value - value: damage type;body site - description: Information about any mechanical damage exerted on the plant; can - include multiple damages and sites - title: mechanical damage + value: FOODON:03510023 + description: These descriptors are used either for foods intended for special + dietary use as defined in 21 CFR 105 or for foods that have special characteristics + indicated in the name or labeling. This field accepts terms listed under dietary + claim or use (http://purl.obolibrary.org/obo/FOODON_03510023). Multiple terms + can be separated by one or more pipes, but please consider limiting this list + to the most prominent dietary claim or use + title: dietary claim or use examples: - - value: pruning;bark + - value: No preservatives [FOODON:03510113] from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text};{text}' - slot_uri: MIXS:0001052 + keywords: + - diet + - use + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001199 multivalued: true required: false recommended: false - medic_hist_perform: - name: medic_hist_perform - description: Whether full medical history was collected - title: medical history performed + diether_lipids: + name: diether_lipids + annotations: + Expected_value: + tag: Expected_value + value: diether lipid name;measurement value + Preferred_unit: + tag: Preferred_unit + value: nanogram per liter + description: Concentration of diether lipids; can include multiple types of diether + lipids + title: diether lipids examples: - - value: '1' + - value: 0.2 nanogram per liter from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - history - slot_uri: MIXS:0000897 - multivalued: false - range: boolean + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000178 + multivalued: true required: false recommended: false - menarche: - name: menarche - description: Date of most recent menstruation - title: menarche + diss_carb_dioxide: + name: diss_carb_dioxide + annotations: + Preferred_unit: + tag: Preferred_unit + value: micromole per liter, milligram per liter + description: Concentration of dissolved carbon dioxide in the sample or liquid + portion of the sample + title: dissolved carbon dioxide examples: - - value: '2013-03-25T12:42:31+01:00' + - value: 5 milligram per liter from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000965 + keywords: + - carbon + - dissolved + slot_uri: MIXS:0000436 multivalued: false - range: datetime + range: string required: false recommended: false - menopause: - name: menopause - description: Date of onset of menopause - title: menopause - examples: - - value: '2013-03-25T12:42:31+01:00' - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000968 - multivalued: false - range: datetime - required: false - recommended: false - methane: - name: methane + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + diss_hydrogen: + name: diss_hydrogen annotations: Preferred_unit: tag: Preferred_unit - value: micromole per liter, parts per billion, parts per million - description: Methane (gas) amount or concentration at the time of sampling - title: methane + value: micromole per liter + description: Concentration of dissolved hydrogen + title: dissolved hydrogen + examples: + - value: 0.3 micromole per liter from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000101 + keywords: + - dissolved + slot_uri: MIXS:0000179 multivalued: false range: string required: false @@ -10439,110 +8547,117 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - micro_biomass_meth: - name: micro_biomass_meth - description: Reference or method used in determining microbial biomass - title: microbial biomass method - comments: - - slot name/scn was microbial_biomass_meth + diss_inorg_carb: + name: diss_inorg_carb + annotations: + Preferred_unit: + tag: Preferred_unit + value: microgram per liter, milligram per liter, parts per million + description: Dissolved inorganic carbon concentration in the sample, typically + measured after filtering the sample using a 0.45 micrometer filter + title: dissolved inorganic carbon examples: - - value: http://dx.doi.org/10.1016/j.soilbio.2005.01.021 + - value: 2059 micromole per kilogram from_schema: https://w3id.org/mixs-6-2-rc keywords: - - biomass - - method - - microbial - slot_uri: MIXS:0000339 + - carbon + - dissolved + - inorganic + slot_uri: MIXS:0000434 + multivalued: false range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - microb_cult_med: - name: microb_cult_med - description: A culture medium used to select for, grow, and maintain prokaryotic - microorganisms. Can be in either liquid (broth) or solidified (e.g. with agar) - forms. This field accepts terms listed under microbiological culture medium - (http://purl.obolibrary.org/obo/MICRO_0000067). If the proper descriptor is - not listed please use text to describe the culture medium - title: microbiological culture medium + diss_inorg_nitro: + name: diss_inorg_nitro + annotations: + Preferred_unit: + tag: Preferred_unit + value: microgram per liter, micromole per liter + description: Concentration of dissolved inorganic nitrogen + title: dissolved inorganic nitrogen examples: - - value: brain heart infusion agar [MICRO:0000566] + - value: 761 micromole per liter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - culture - - microbiological - slot_uri: MIXS:0001216 + - dissolved + - inorganic + - nitrogen + slot_uri: MIXS:0000698 multivalued: false range: string required: false recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$ + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{text}|({termLabel} \[{termID}\])$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - microb_start: - name: microb_start - annotations: - Expected_value: - tag: Expected_value - value: FOODON:03544453 - description: Any type of microorganisms used in food production. This field accepts - terms listed under live organisms for food production (http://purl.obolibrary.org/obo/FOODON_0344453) - title: microbial starter + diss_inorg_phosp: + name: diss_inorg_phosp + description: Concentration of dissolved inorganic phosphorus in the sample + title: dissolved inorganic phosphorus examples: - - value: starter cultures [FOODON:03544454] + - value: 56.5 micromole per liter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - microbial - string_serialization: '{term label} [{termID}]|{text}' - slot_uri: MIXS:0001217 + - dissolved + - inorganic + - phosphorus + slot_uri: MIXS:0000106 multivalued: false - required: false - recommended: false - microb_start_count: - name: microb_start_count + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + diss_iron: + name: diss_iron annotations: - Expected_value: - tag: Expected_value - value: organism name; measurement value; enumeration Preferred_unit: tag: Preferred_unit - value: colony forming units per milliliter; colony forming units per gram - of dry weight - description: 'Total cell count of starter culture per gram, volume or area of - sample and the method that was used for the enumeration (e.g. qPCR, atp, mpn, - etc.) should also be provided. (example : total prokaryotes; 3.5e7 cells per - ml; qPCR)' - title: microbial starter organism count - examples: - - value: total prokaryotes;3.5e9 colony forming units per milliliter;spread plate + value: milligram per liter + description: Concentration of dissolved iron in the sample + title: dissolved iron from_schema: https://w3id.org/mixs-6-2-rc keywords: - - count - - microbial - - organism - string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|spread plate|other]' - slot_uri: MIXS:0001218 + - dissolved + slot_uri: MIXS:0000139 multivalued: false - required: false - recommended: false - microb_start_inoc: - name: microb_start_inoc + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + diss_org_carb: + name: diss_org_carb annotations: Preferred_unit: tag: Preferred_unit - value: milligram or gram - description: The amount of starter culture used to inoculate a new batch - title: microbial starter inoculation + value: micromole per liter, milligram per liter + description: Concentration of dissolved organic carbon in the sample, liquid portion + of the sample, or aqueous phase of the fluid + title: dissolved organic carbon examples: - - value: 100 milligrams + - value: 197 micromole per liter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - microbial - slot_uri: MIXS:0001219 + - carbon + - dissolved + - organic + slot_uri: MIXS:0000433 multivalued: false range: string required: false @@ -10553,255 +8668,195 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - microb_start_prep: - name: microb_start_prep - description: Information about the protocol or method used to prepare the starter - inoculum - title: microbial starter preparation - examples: - - value: liquid starter culture, propagated 3 cycles in milk prior to inoculation - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - microbial - - preparation - slot_uri: MIXS:0001220 - multivalued: false - range: string - required: false - recommended: false - microb_start_source: - name: microb_start_source - description: The source from which the microbial starter culture was sourced. If - commercially supplied, list supplier - title: microbial starter source + diss_org_nitro: + name: diss_org_nitro + description: Dissolved organic nitrogen concentration measured as; total dissolved + nitrogen - NH4 - NO3 - NO2 + title: dissolved organic nitrogen examples: - - value: backslopped, GetCulture + - value: 0.05 micromole per liter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - microbial - - source - slot_uri: MIXS:0001221 + - dissolved + - nitrogen + - organic + slot_uri: MIXS:0000162 multivalued: false range: string required: false recommended: false - microb_start_taxID: - name: microb_start_taxID - description: Please include Genus species and strain ID, if known of microorganisms - used in food production. For complex communities, pipes can be used to separate - two or more microbes - title: microbial starter NCBI taxonomy ID + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + diss_oxygen: + name: diss_oxygen + annotations: + Preferred_unit: + tag: Preferred_unit + value: micromole per kilogram, milligram per liter + description: Concentration of dissolved oxygen + title: dissolved oxygen examples: - - value: Lactobacillus rhamnosus [NCIT:C123495] + - value: 175 micromole per kilogram from_schema: https://w3id.org/mixs-6-2-rc keywords: - - identifier - - microbial - - ncbi - - taxon - slot_uri: MIXS:0001222 + - dissolved + - oxygen + slot_uri: MIXS:0000119 multivalued: false range: string required: false recommended: false - pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^({termLabel} \[{termID}\])|{integer}$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - microbial_biomass: - name: microbial_biomass + diss_oxygen_fluid: + name: diss_oxygen_fluid annotations: Preferred_unit: tag: Preferred_unit - value: ton, kilogram, gram per kilogram soil - description: The part of the organic matter in the soil that constitutes living - microorganisms smaller than 5-10 micrometer. If you keep this, you would need - to have correction factors used for conversion to the final units - title: microbial biomass + value: micromole per kilogram, milligram per liter + description: Concentration of dissolved oxygen in the oil field produced fluids + as it contributes to oxgen-corrosion and microbial activity (e.g. Mic) + title: dissolved oxygen in fluids from_schema: https://w3id.org/mixs-6-2-rc keywords: - - biomass - - microbial - slot_uri: MIXS:0000650 + - dissolved + - oxygen + slot_uri: MIXS:0000438 multivalued: false range: string + required: false + recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - mid: - name: mid - description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are - used to specifically tag unique samples in a sequencing run. Sequence should - be reported in uppercase letters - title: multiplex identifiers + dominant_hand: + name: dominant_hand + description: Dominant hand of the subject + title: dominant hand examples: - - value: GTGAATAT - in_subset: - - sequencing + - value: right from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - identifier - slot_uri: MIXS:0000047 + slot_uri: MIXS:0000944 multivalued: false - range: string - pattern: ^[ACGTRKSYMWBHDVN]+$ - structured_pattern: - syntax: ^{ambiguous_nucleotides}$ - interpolated: true - partial_match: true - mineral_nutr_regm: - name: mineral_nutr_regm - annotations: - Expected_value: - tag: Expected_value - value: mineral nutrient name;mineral nutrient amount;treatment interval and - duration - Preferred_unit: - tag: Preferred_unit - value: gram, mole per liter, milligram per liter - description: Information about treatment involving the use of mineral supplements; - should include the name of mineral nutrient, amount administered, treatment - regimen including how many times the treatment was repeated, how long each treatment - lasted, and the start and end time of the entire treatment; can include multiple - mineral nutrient regimens - title: mineral nutrient regimen + range: DOMINANT_HAND_ENUM + required: false + recommended: false + door_comp_type: + name: door_comp_type + description: The composite type of the door + title: door type, composite examples: - - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: revolving from_schema: https://w3id.org/mixs-6-2-rc keywords: - - mineral - - nutrient - - regimen - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000570 - multivalued: true + - door + - type + slot_uri: MIXS:0000795 + multivalued: false + range: DOOR_COMP_TYPE_ENUM required: false recommended: false - misc_param: - name: misc_param - annotations: - Expected_value: - tag: Expected_value - value: parameter name;measurement value - description: Any other measurement performed or parameter collected, that is not - listed here - title: miscellaneous parameter + door_cond: + name: door_cond + description: The phsical condition of the door + title: door condition examples: - - value: Bicarbonate ion concentration;2075 micromole per kilogram + - value: new from_schema: https://w3id.org/mixs-6-2-rc keywords: - - parameter - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000752 - multivalued: true + - condition + - door + slot_uri: MIXS:0000788 + multivalued: false + range: SHARED_ENUM_2 required: false recommended: false - mode_transmission: - name: mode_transmission - description: The process through which the symbiotic host organism entered the - host from which it was sampled - title: mode of transmission - examples: - - value: horizontal:castrator - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0001312 - range: MODE_TRANSMISSION_ENUM - recommended: true - n_alkanes: - name: n_alkanes - annotations: - Expected_value: - tag: Expected_value - value: n-alkane name;measurement value - description: Concentration of n-alkanes; can include multiple n-alkanes - title: n-alkanes + door_direct: + name: door_direct + description: The direction the door opens + title: door direction of opening examples: - - value: n-hexadecane;100 milligram per liter + - value: inward from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000503 - multivalued: true + keywords: + - direction + - door + slot_uri: MIXS:0000789 + multivalued: false + range: DOOR_DIRECT_ENUM required: false recommended: false - neg_cont_type: - name: neg_cont_type - annotations: - Expected_value: - tag: Expected_value - value: enumeration or text - description: The substance or equipment used as a negative control in an investigation - title: negative control type - in_subset: - - investigation + door_loc: + name: door_loc + description: The relative location of the door in the room + title: door location + examples: + - value: north from_schema: https://w3id.org/mixs-6-2-rc keywords: - - type - slot_uri: MIXS:0001321 + - door + - location + slot_uri: MIXS:0000790 multivalued: false - range: NEG_CONT_TYPE_ENUM - recommended: true - nitrate: - name: nitrate - annotations: - Preferred_unit: - tag: Preferred_unit - value: micromole per liter, milligram per liter, parts per million - description: Concentration of nitrate in the sample - title: nitrate + range: SHARED_ENUM_0 + required: false + recommended: false + door_mat: + name: door_mat + description: The material the door is composed of + title: door material examples: - - value: 65 micromole per liter + - value: wood from_schema: https://w3id.org/mixs-6-2-rc keywords: - - nitrate - slot_uri: MIXS:0000425 + - door + - material + slot_uri: MIXS:0000791 multivalued: false - range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - nitrite: - name: nitrite - annotations: - Preferred_unit: - tag: Preferred_unit - value: micromole per liter, milligram per liter, parts per million - description: Concentration of nitrite in the sample - title: nitrite + range: DOOR_MAT_ENUM + required: false + recommended: false + door_move: + name: door_move + description: The type of movement of the door + title: door movement examples: - - value: 0.5 micromole per liter + - value: swinging from_schema: https://w3id.org/mixs-6-2-rc keywords: - - nitrite - slot_uri: MIXS:0000426 + - door + slot_uri: MIXS:0000792 multivalued: false - range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - nitro: - name: nitro + range: DOOR_MOVE_ENUM + required: false + recommended: false + door_size: + name: door_size annotations: Preferred_unit: tag: Preferred_unit - value: micromole per liter - description: Concentration of nitrogen (total) - title: nitrogen + value: square meter + description: The size of the door + title: door area or size examples: - - value: 4.2 micromole per liter + - value: 2.5 square meter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - nitrogen - slot_uri: MIXS:0000504 + - area + - door + - size + slot_uri: MIXS:0000158 multivalued: false range: string required: false @@ -10812,148 +8867,166 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - non_min_nutr_regm: - name: non_min_nutr_regm - annotations: - Preferred_unit: - tag: Preferred_unit - value: gram, mole per liter, milligram per liter - description: Information about treatment involving the exposure of plant to non-mineral - nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral - nutrient, amount administered, treatment regimen including how many times the - treatment was repeated, how long each treatment lasted, and the start and end - time of the entire treatment; can include multiple non-mineral nutrient regimens - title: non-mineral nutrient regimen + door_type: + name: door_type + description: The type of door material + title: door type examples: - - value: https://phylogenomics.me/protocols/16s-pcr-protocol/ + - value: wooden from_schema: https://w3id.org/mixs-6-2-rc keywords: - - non-mineral - - nutrient - - regimen - slot_uri: MIXS:0000571 - multivalued: true - range: string - nose_mouth_teeth_throat_disord: - name: nose_mouth_teeth_throat_disord - description: History of nose/mouth/teeth/throat disorders; can include multiple - disorders. The terms should be chosen from the DO (Human Disease Ontology) at - http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), - mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), - or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974) - title: nose/mouth/teeth/throat disorder + - door + - type + slot_uri: MIXS:0000794 + multivalued: false + range: DOOR_TYPE_ENUM + required: false + recommended: false + door_type_metal: + name: door_type_metal + description: The type of metal door + title: door type, metal + examples: + - value: hollow from_schema: https://w3id.org/mixs-6-2-rc keywords: - - disorder - slot_uri: MIXS:0000283 - multivalued: true - range: string + - door + - type + slot_uri: MIXS:0000796 + multivalued: false + range: DOOR_TYPE_METAL_ENUM required: false recommended: false - nose_throat_disord: - name: nose_throat_disord - description: History of nose-throat disorders; can include multiple disorders, The - terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory - tract disease (https://disease-ontology.org/?id=DOID:974) - title: nose throat disorder + door_type_wood: + name: door_type_wood + annotations: + Expected_value: + tag: Expected_value + value: enumeration + description: The type of wood door + title: door type, wood + examples: + - value: battened from_schema: https://w3id.org/mixs-6-2-rc keywords: - - disorder - slot_uri: MIXS:0000270 - multivalued: true - range: string + - door + - type + string_serialization: '[bettened and ledged|battened|ledged and braced|battened|ledged + and framed|battened|ledged, braced and frame|framed and paneled|glashed or sash|flush|louvered|wire + gauged]' + slot_uri: MIXS:0000797 + multivalued: false required: false recommended: false - nucl_acid_amp: - name: nucl_acid_amp - description: A link to a literature reference, electronic resource or a standard - operating procedure (SOP), that describes the enzymatic amplification (PCR, - TMA, NASBA) of specific nucleic acids - title: nucleic acid amplification + door_water_mold: + name: door_water_mold + description: Signs of the presence of mold or mildew on a door + title: door signs of water/mold examples: - - value: https://phylogenomics.me/protocols/16s-pcr-protocol/ - in_subset: - - sequencing + - value: presence of mold visible from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000038 + keywords: + - door + slot_uri: MIXS:0000793 multivalued: false - range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ - structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ - interpolated: true - partial_match: true - nucl_acid_ext: - name: nucl_acid_ext - description: A link to a literature reference, electronic resource or a standard - operating procedure (SOP), that describes the material separation to recover - the nucleic acid fraction from a sample - title: nucleic acid extraction + range: SHARED_ENUM_1 + required: false + recommended: false + douche: + name: douche + description: Date of most recent douche + title: douche examples: - - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf - in_subset: - - sequencing + - value: '2013-03-25T12:42:31+01:00' from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000037 + slot_uri: MIXS:0000967 + multivalued: false + range: datetime + required: false + recommended: false + down_par: + name: down_par + annotations: + Preferred_unit: + tag: Preferred_unit + value: microEinstein per square meter per second, microEinstein per square + centimeter per second + description: Visible waveband radiance and irradiance measurements in the water + column + title: downward PAR + examples: + - value: 28.71 microEinstein per square meter per second + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000703 multivalued: false range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - nucl_acid_ext_kit: - name: nucl_acid_ext_kit - annotations: - Expected_value: - tag: Expected_value - value: The name of an extraction kit - description: The name of the extraction kit used to recover the nucleic acid fraction - of an input material is performed - title: nucleic acid extraction kit + drainage_class: + name: drainage_class + description: Drainage classification from a standard system such as the USDA system + title: drainage classification examples: - - value: Qiagen PowerSoil Kit + - value: well from_schema: https://w3id.org/mixs-6-2-rc keywords: - - kit - string_serialization: '{text}' - slot_uri: MIXS:0001223 - multivalued: true + - classification + slot_uri: MIXS:0001085 + multivalued: false + range: DRAINAGE_CLASS_ENUM + drawings: + name: drawings + description: The buildings architectural drawings; if design is chosen, indicate + phase-conceptual, schematic, design development, and construction documents + title: drawings + examples: + - value: sketch + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - drawings + slot_uri: MIXS:0000798 + multivalued: false + range: DRAWINGS_ENUM required: false recommended: false - num_replicons: - name: num_replicons + drug_usage: + name: drug_usage annotations: Expected_value: tag: Expected_value - value: 'for eukaryotes and bacteria: chromosomes (haploid count); for viruses: - segments' - description: Reports the number of replicons in a nuclear genome of eukaryotes, - in the genome of a bacterium or archaea or the number of segments in a segmented - virus. Always applied to the haploid chromosome count of a eukaryote - title: number of replicons + value: drug name;frequency + description: Any drug used by subject and the frequency of usage; can include + multiple drugs used + title: drug usage examples: - - value: '2' - in_subset: - - nucleic acid sequence source + - value: Lipitor;2/day from_schema: https://w3id.org/mixs-6-2-rc keywords: - - number - string_serialization: '{integer}' - slot_uri: MIXS:0000022 - range: integer - num_samp_collect: - name: num_samp_collect - description: The number of samples collected during the current sampling event - title: number of samples collected - examples: - - value: 116 samples + - drug + - use + string_serialization: '{text};{integer}/[year|month|week|day|hour]' + slot_uri: MIXS:0000894 + multivalued: true + required: false + recommended: false + efficiency_percent: + name: efficiency_percent + annotations: + Preferred_unit: + tag: Preferred_unit + value: micromole per liter + description: Percentage of volatile solids removed from the anaerobic digestor + title: efficiency percent from_schema: https://w3id.org/mixs-6-2-rc keywords: - - number - - sample - slot_uri: MIXS:0001224 + - percent + slot_uri: MIXS:0000657 multivalued: false range: string required: false @@ -10964,360 +9037,288 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - number_contig: - name: number_contig - description: Total number of contigs in the cleaned/submitted assembly that makes - up a given genome, SAG, MAG, or UViG - title: number of contigs + elev: + name: elev + annotations: + Preferred_unit: + tag: Preferred_unit + value: meter + description: Elevation of the sampling site is its height above a fixed reference + point, most commonly the mean sea level. Elevation is mainly used when referring + to points on the earth's surface, while altitude is used for points above the + surface, such as an aircraft in flight or a spacecraft in orbit + title: elevation examples: - - value: '40' + - value: 100 meter in_subset: - - sequencing - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - number - slot_uri: MIXS:0000060 - multivalued: false - range: integer - number_pets: - name: number_pets - description: The number of pets residing in the sampled space - title: number of pets + - environment from_schema: https://w3id.org/mixs-6-2-rc keywords: - - number - slot_uri: MIXS:0000231 + - elevation + slot_uri: MIXS:0000093 multivalued: false range: string - required: false - recommended: false - pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{integer} {text}$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - number_plants: - name: number_plants - description: The number of plant(s) in the sampling space - title: number of houseplants + elevator: + name: elevator + description: The number of elevators within the built structure + title: elevator count + examples: + - value: '2' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - number - slot_uri: MIXS:0000230 + - count + slot_uri: MIXS:0000799 multivalued: false - range: string + range: integer required: false recommended: false - pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{integer} {text}$ - interpolated: true - partial_match: true - number_resident: - name: number_resident - description: The number of individuals currently occupying in the sampling location - title: number of residents + emulsions: + name: emulsions + annotations: + Expected_value: + tag: Expected_value + value: emulsion name;measurement value + Preferred_unit: + tag: Preferred_unit + value: gram per liter + description: Amount or concentration of substances such as paints, adhesives, + mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion + types + title: emulsions from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - number - slot_uri: MIXS:0000232 - multivalued: false - range: string + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000660 + multivalued: true required: false recommended: false - pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{integer} {text}$ - interpolated: true - partial_match: true - occup_density_samp: - name: occup_density_samp - description: Average number of occupants at time of sampling per square footage - title: occupant density at sampling + encoded_traits: + name: encoded_traits + annotations: + Expected_value: + tag: Expected_value + value: 'for plasmid: antibiotic resistance; for phage: converting genes' + description: Should include key traits like antibiotic resistance or xenobiotic + degradation phenotypes for plasmids, converting genes for phage + title: encoded traits examples: - - value: '0.1' + - value: beta-lactamase class A + in_subset: + - nucleic acid sequence source from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - density - slot_uri: MIXS:0000217 + string_serialization: '{text}' + slot_uri: MIXS:0000034 multivalued: false - range: float - required: true - occup_document: - name: occup_document - description: The type of documentation of occupancy - title: occupancy documentation + enrichment_protocol: + name: enrichment_protocol + description: The microbiological workflow or protocol followed to test for the + presence or enumeration of the target microbial analyte(s). Please provide a + PubMed or DOI reference for published protocols + title: enrichment protocol examples: - - value: estimate + - value: 'BAM Chapter 4: Enumeration of Escherichia coli and the Coliform Bacteria' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - documentation - slot_uri: MIXS:0000816 + - enrichment + - protocol + slot_uri: MIXS:0001177 multivalued: false - range: OCCUP_DOCUMENT_ENUM - required: false - recommended: false - occup_samp: - name: occup_samp - description: Number of occupants present at time of sample within the given space - title: occupancy at sampling - examples: - - value: '10' - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000772 - range: float - required: true - pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{integer} {text}$ + syntax: ^{PMID}|{DOI}|{URL}|{text}$ interpolated: true partial_match: true - org_carb: - name: org_carb - description: Concentration of organic carbon - title: organic carbon + env_broad_scale: + name: env_broad_scale + description: 'Report the major environmental system the sample or specimen came + from. The system(s) identified should have a coarse spatial grain, to provide + the general environmental context of where the sampling was done (e.g. in the + desert or a rainforest). We recommend using subclasses of EnvO s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. + EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS' + title: broad-scale environmental context examples: - - value: 1.5 microgram per liter + - value: rangeland biome [ENVO:01000247] + in_subset: + - environment from_schema: https://w3id.org/mixs-6-2-rc keywords: - - carbon - - organic - slot_uri: MIXS:0000508 + - context + - environmental + slot_uri: MIXS:0000012 multivalued: false range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + required: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: ^{termLabel} \[{termID}\]$ interpolated: true partial_match: true - org_count_qpcr_info: - name: org_count_qpcr_info + env_local_scale: + name: env_local_scale annotations: Expected_value: tag: Expected_value - value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial - denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final - elongation:degrees_minutes; total cycles - Preferred_unit: - tag: Preferred_unit - value: number of cells per gram (or ml or cm^2) - description: 'If qpcr was used for the cell count, the target gene name, the primer - sequence and the cycling conditions should also be provided. (Example: 16S rrna; - FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; - annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; - 30 cycles)' - title: organism count qPCR information - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - count - - information - - organism - string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final - elongation:degrees_minutes; total cycles' - slot_uri: MIXS:0000099 - multivalued: false - required: false - recommended: false - org_matter: - name: org_matter - annotations: - Preferred_unit: - tag: Preferred_unit - value: microgram per liter - description: Concentration of organic matter - title: organic matter + value: Environmental entities having causal influences upon the entity at + time of sampling + description: 'Report the entity or entities which are in the sample or specimen + s local vicinity and which you believe have significant causal influences on + your sample or specimen. We recommend using EnvO terms which are of smaller + spatial grain than your entry for env_broad_scale. Terms, such as anatomical + sites, from other OBO Library ontologies which interoperate with EnvO (e.g. + UBERON) are accepted in this field. EnvO documentation about how to use the + field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS' + title: local environmental context examples: - - value: 1.75 milligram per cubic meter + - value: hillside [ENVO:01000333] + in_subset: + - environment from_schema: https://w3id.org/mixs-6-2-rc keywords: - - organic - slot_uri: MIXS:0000204 + - context + - environmental + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0000013 multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - org_nitro: - name: org_nitro - description: Concentration of organic nitrogen - title: organic nitrogen + required: true + env_medium: + name: env_medium + description: 'Report the environmental material(s) immediately surrounding the + sample or specimen at the time of sampling. We recommend using subclasses of + ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO + documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS + . Terms from other OBO ontologies are permissible as long as they reference + mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities + (e.g. a tree, a leaf, a table top)' + title: environmental medium examples: - - value: 4 micromole per liter + - value: bluegrass field soil [ENVO:00005789] + in_subset: + - environment from_schema: https://w3id.org/mixs-6-2-rc keywords: - - nitrogen - - organic - slot_uri: MIXS:0000205 + - environmental + slot_uri: MIXS:0000014 multivalued: false range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + required: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: ^{termLabel} \[{termID}\]$ interpolated: true partial_match: true - org_particles: - name: org_particles + env_monitoring_zone: + name: env_monitoring_zone annotations: Expected_value: tag: Expected_value - value: particle name;measurement value - Preferred_unit: - tag: Preferred_unit - value: gram per liter - description: Concentration of particles such as faeces, hairs, food, vomit, paper - fibers, plant material, humus, etc - title: organic particles + value: ENVO + description: An environmental monitoring zone is a formal designation as part + of an environmental monitoring program, in which areas of a food production + facility are categorized, commonly as zones 1-4, based on likelihood or risk + of foodborne pathogen contamination. This field accepts terms listed under food + production environmental monitoring zone (http://purl.obolibrary.org/obo/ENVO). + Please add a term to indicate the environmental monitoring zone the sample was + taken from + title: food production environmental monitoring zone + examples: + - value: Zone 1 from_schema: https://w3id.org/mixs-6-2-rc keywords: - - organic - - particle - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000665 - multivalued: true + - environmental + - food + - production + string_serialization: '{text}' + slot_uri: MIXS:0001254 + multivalued: false required: false recommended: false - organism_count: - name: organism_count - annotations: - Expected_value: - tag: Expected_value - value: organism name;measurement value;enumeration - description: 'Total cell count of any organism (or group of organisms) per gram, - volume or area of sample, should include name of organism followed by count. - The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should - also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)' - title: organism count - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - count - - organism - string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]' - slot_uri: MIXS:0000103 - multivalued: true - otu_class_appr: - name: otu_class_appr - annotations: - Expected_value: - tag: Expected_value - value: cutoffs and method used - description: Cutoffs and approach used when clustering species-level OTUs. Note - that results from standard 95% ANI / 85% AF clustering should be provided alongside - OTUS defined from another set of thresholds, even if the latter are the ones - primarily used during the analysis - title: OTU classification approach + escalator: + name: escalator + description: The number of escalators within the built structure + title: escalator count examples: - - value: 95% ANI;85% AF; greedy incremental clustering - in_subset: - - sequencing + - value: '4' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - classification - - otu - string_serialization: '{ANI cutoff};{AF cutoff};{clustering method}' - slot_uri: MIXS:0000085 + - count + slot_uri: MIXS:0000800 multivalued: false - otu_db: - name: otu_db + range: integer + required: false + recommended: false + estimated_size: + name: estimated_size annotations: Expected_value: tag: Expected_value - value: database and version - description: Reference database (i.e. sequences not generated as part of the current - study) used to cluster new genomes in "species-level" OTUs, if any - title: OTU database + value: number of base pairs + description: The estimated size of the genome prior to sequencing. Of particular + importance in the sequencing of (eukaryotic) genome which could remain in draft + form for a long or unspecified period + title: estimated size examples: - - value: NCBI Viral RefSeq;83 + - value: 300000 bp in_subset: - - sequencing + - nucleic acid sequence source from_schema: https://w3id.org/mixs-6-2-rc keywords: - - database - - otu - string_serialization: '{database};{version}' - slot_uri: MIXS:0000087 + - size + string_serialization: '{integer} bp' + slot_uri: MIXS:0000024 multivalued: false - otu_seq_comp_appr: - name: otu_seq_comp_appr + ethnicity: + name: ethnicity annotations: Expected_value: tag: Expected_value - value: software name, version and relevant parameters - description: Tool and thresholds used to compare sequences when computing "species-level" - OTUs - title: OTU sequence comparison approach + value: text recommend from Wikipedia list + description: A category of people who identify with each other, usually on the + basis of presumed similarities such as a common language, ancestry, history, + society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups + title: ethnicity examples: - - value: 'blastn;2.6.0+;e-value cutoff: 0.001' - in_subset: - - sequencing + - value: native american from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - otu - string_serialization: '{software};{version};{parameters}' - slot_uri: MIXS:0000086 - multivalued: false - owc_tvdss: - name: owc_tvdss + string_serialization: '{text}' + slot_uri: MIXS:0000895 + multivalued: true + required: false + recommended: false + ethylbenzene: + name: ethylbenzene annotations: Preferred_unit: tag: Preferred_unit - value: meter - description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) - title: oil water contact depth + value: milligram per liter, parts per million + description: Concentration of ethylbenzene in the sample + title: ethylbenzene from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - depth - - oil - - water - slot_uri: MIXS:0000405 + slot_uri: MIXS:0000155 multivalued: false range: string - required: false - recommended: false + recommended: true pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - oxy_stat_samp: - name: oxy_stat_samp - description: Oxygenation status of sample - title: oxygenation status of sample - examples: - - value: aerobic - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - oxygen - - sample - - status - slot_uri: MIXS:0000753 - multivalued: false - range: OXY_STAT_SAMP_ENUM - oxygen: - name: oxygen + exp_duct: + name: exp_duct annotations: Preferred_unit: tag: Preferred_unit - value: milligram per liter, parts per million - description: Oxygen (gas) amount or concentration at the time of sampling - title: oxygen - examples: - - value: 600 parts per million + value: square meter + description: The amount of exposed ductwork in the room + title: exposed ductwork from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - oxygen - slot_uri: MIXS:0000104 + slot_uri: MIXS:0000144 multivalued: false range: string required: false @@ -11328,406 +9329,412 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - part_org_carb: - name: part_org_carb - description: Concentration of particulate organic carbon - title: particulate organic carbon - examples: - - value: 1.92 micromole per liter + exp_pipe: + name: exp_pipe + description: The number of exposed pipes in the room + title: exposed pipes from_schema: https://w3id.org/mixs-6-2-rc keywords: - - carbon - - organic - - particle - - particulate - slot_uri: MIXS:0000515 + - pipes + slot_uri: MIXS:0000220 multivalued: false range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: ^{integer} {text}$ interpolated: true partial_match: true - part_org_nitro: - name: part_org_nitro + experimental_factor: + name: experimental_factor annotations: - Preferred_unit: - tag: Preferred_unit - value: microgram per liter, micromole per liter - description: Concentration of particulate organic nitrogen - title: particulate organic nitrogen + Expected_value: + tag: Expected_value + value: text or EFO and/or OBI + description: Variable aspects of an experiment design that can be used to describe + an experiment, or set of experiments, in an increasingly detailed manner. This + field accepts ontology terms from Experimental Factor Ontology (EFO) and/or + Ontology for Biomedical Investigations (OBI) + title: experimental factor examples: - - value: 0.3 micromole per liter + - value: time series design [EFO:0001779] + in_subset: + - investigation from_schema: https://w3id.org/mixs-6-2-rc keywords: - - nitrogen - - organic - - particle - - particulate - slot_uri: MIXS:0000719 - multivalued: false + - experimental + - factor + string_serialization: '{termLabel} [{termID}]|{text}' + slot_uri: MIXS:0000008 + multivalued: true range: string + pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ + ext_door: + name: ext_door + description: The number of exterior doors in the built structure + title: exterior door count + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - count + - door + - exterior + slot_uri: MIXS:0000170 + multivalued: false + range: integer required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - part_plant_animal: - name: part_plant_animal - annotations: - Expected_value: - tag: Expected_value - value: FOODON:03420116 - description: The anatomical part of the organism being involved in food production - or consumption; e.g., a carrot is the root of the plant (root vegetable). This - field accepts terms listed under part of plant or animal (http://purl.obolibrary.org/obo/FOODON_03420116) - title: part of plant or animal + ext_wall_orient: + name: ext_wall_orient + description: The orientation of the exterior wall + title: orientations of exterior wall examples: - - value: chuck [FOODON:03530021] + - value: northwest from_schema: https://w3id.org/mixs-6-2-rc keywords: - - animal - - plant - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001149 - multivalued: true + - exterior + - wall + slot_uri: MIXS:0000817 + multivalued: false + range: SHARED_ENUM_0 required: false recommended: false - particle_class: - name: particle_class - annotations: - Expected_value: - tag: Expected_value - value: particle name;measurement value - Preferred_unit: - tag: Preferred_unit - value: micrometer - description: Particles are classified, based on their size, into six general categories:clay, - silt, sand, gravel, cobbles, and boulders; should include amount of particle - preceded by the name of the particle type; can include multiple values - title: particle classification + ext_window_orient: + name: ext_window_orient + description: The compass direction the exterior window of the room is facing + title: orientations of exterior window + examples: + - value: southwest from_schema: https://w3id.org/mixs-6-2-rc keywords: - - classification - - particle - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000206 + - exterior + - window + slot_uri: MIXS:0000818 + multivalued: false + range: SHARED_ENUM_0 + required: false + recommended: false + extr_weather_event: + name: extr_weather_event + description: Unusual weather events that may have affected microbial populations. + Multiple terms can be separated by pipes, listed in reverse chronological order + title: extreme weather event + examples: + - value: hail + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - event + - extreme + - weather + slot_uri: MIXS:0001141 multivalued: true + range: EXTR_WEATHER_EVENT_ENUM required: false recommended: false - pathogenicity: - name: pathogenicity - annotations: - Expected_value: - tag: Expected_value - value: names of organisms that the entity is pathogenic to - description: To what is the entity pathogenic - title: known pathogenicity + extrachrom_elements: + name: extrachrom_elements + description: Do plasmids exist of significant phenotypic consequence (e.g. ones + that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids + (borrelia has 15+ plasmids) + title: extrachromosomal elements examples: - - value: human, animal, plant, fungi, bacteria + - value: '5' in_subset: - nucleic acid sequence source from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text}' - slot_uri: MIXS:0000027 + slot_uri: MIXS:0000023 multivalued: false - pcr_cond: - name: pcr_cond - annotations: - Expected_value: - tag: Expected_value - value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final - elongation:degrees_minutes;total cycles - description: Description of reaction conditions and components of PCR in the form - of 'initial denaturation:94degC_1.5min; annealing=...' - title: pcr conditions - examples: - - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 - in_subset: - - sequencing + range: integer + extreme_event: + name: extreme_event + description: Unusual physical events that may have affected microbial populations + title: history/extreme events from_schema: https://w3id.org/mixs-6-2-rc keywords: - - condition - - pcr - string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final - elongation:degrees_minutes;total cycles - slot_uri: MIXS:0000049 + - event + - history + slot_uri: MIXS:0000320 multivalued: false - pcr_primers: - name: pcr_primers - annotations: - Expected_value: - tag: Expected_value - value: 'FWD: forward primer sequence;REV:reverse primer sequence' - description: PCR primers that were used to amplify the sequence of the targeted - gene, locus or subfragment. This field should contain all the primers used for - a single PCR reaction if multiple forward or reverse primers are present in - a single PCR reaction. The primer sequence should be reported in uppercase letters - title: pcr primers + range: datetime + facility_type: + name: facility_type + description: Establishment details about the type of facility where the sample + was taken. This is independent of the specific product(s) within the facility + title: facility type examples: - - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT - in_subset: - - sequencing + - value: manufacturing-processing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - pcr - string_serialization: FWD:{dna};REV:{dna} - slot_uri: MIXS:0000046 - multivalued: false - permeability: - name: permeability - annotations: - Expected_value: - tag: Expected_value - value: measurement value range - Preferred_unit: - tag: Preferred_unit - value: mD - description: 'Measure of the ability of a hydrocarbon resource to allow fluids - to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))' - title: permeability - from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{integer} - {integer} {unit}' - slot_uri: MIXS:0000404 - multivalued: false + - facility + - type + slot_uri: MIXS:0001252 + multivalued: true + range: FACILITY_TYPE_ENUM required: false recommended: false - perturbation: - name: perturbation - annotations: - Expected_value: - tag: Expected_value - value: perturbation type name;perturbation interval and duration - description: Type of perturbation, e.g. chemical administration, physical disturbance, - etc., coupled with perturbation regimen including how many times the perturbation - was repeated, how long each perturbation lasted, and the start and end time - of the entire perturbation period; can include multiple perturbation types - title: perturbation + fao_class: + name: fao_class + description: Soil classification from the FAO World Reference Database for Soil + Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups + title: soil_taxonomic/FAO classification examples: - - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M + - value: Luvisols from_schema: https://w3id.org/mixs-6-2-rc keywords: - - perturbation - string_serialization: '{text};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000754 - multivalued: true - pesticide_regm: - name: pesticide_regm - annotations: - Preferred_unit: - tag: Preferred_unit - value: gram, mole per liter, milligram per liter - description: Information about treatment involving use of insecticides; should - include the name of pesticide, amount administered, treatment regimen including - how many times the treatment was repeated, how long each treatment lasted, and - the start and end time of the entire treatment; can include multiple pesticide - regimens - title: pesticide regimen + - classification + slot_uri: MIXS:0001083 + multivalued: false + range: FAO_CLASS_ENUM + farm_equip: + name: farm_equip + description: List of equipment used for planting, fertilization, harvesting, irrigation, + land levelling, residue management, weeding or transplanting during the growing + season. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). + Multiple terms can be separated by pipes + title: farm equipment used examples: - - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: combine harvester [AGRO:00000473] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - regimen - slot_uri: MIXS:0000573 + - equipment + - farm + - use + slot_uri: MIXS:0001126 multivalued: true range: string - pet_farm_animal: - name: pet_farm_animal + required: false + recommended: false + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + farm_equip_san: + name: farm_equip_san annotations: Expected_value: tag: Expected_value - value: presence status;type of animal or pet - description: Specification of presence of pets or farm animals in the environment - of subject, if yes the animals should be specified; can include multiple animals - present - title: presence of pets or farm animals + value: text or commercial name of sanitizer or class of sanitizer or active + ingredient in sanitizer + Preferred_unit: + tag: Preferred_unit + value: parts per million + description: Method used to sanitize growing and harvesting equipment. This can + including type and concentration of sanitizing solution. Multiple terms can + be separated by one or more pipes + title: farm equipment sanitization examples: - - value: yes; 5 cats + - value: hot water pressure wash, hypochlorite solution, 50 parts per million from_schema: https://w3id.org/mixs-6-2-rc keywords: - - animal + - equipment - farm - - presence - string_serialization: '{boolean};{text}' - slot_uri: MIXS:0000267 + string_serialization: '{text} {float} {unit}' + slot_uri: MIXS:0001124 multivalued: true required: false recommended: false - petroleum_hydrocarb: - name: petroleum_hydrocarb - annotations: - Preferred_unit: - tag: Preferred_unit - value: micromole per liter - description: Concentration of petroleum hydrocarbon - title: petroleum hydrocarbon + farm_equip_san_freq: + name: farm_equip_san_freq + description: The number of times farm equipment is cleaned. Frequency of cleaning + might be on a Daily basis, Weekly, Monthly, Quarterly or Annually + title: farm equipment sanitization frequency examples: - - value: 0.05 micromole per liter + - value: Biweekly from_schema: https://w3id.org/mixs-6-2-rc keywords: - - hydrocarbon - - petroleum - slot_uri: MIXS:0000516 + - equipment + - farm + - frequency + slot_uri: MIXS:0001125 multivalued: false range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - ph: - name: ph - description: Ph measurement of the sample, or liquid portion of sample, or aqueous - phase of the fluid - title: pH - examples: - - value: '7.2' + farm_equip_shared: + name: farm_equip_shared + description: List of planting, growing or harvesting equipment shared with other + farms. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). + Multiple terms can be separated by pipes + title: equipment shared with other farms + examples: + - value: combine harvester [AGRO:00000473] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - ph - slot_uri: MIXS:0001001 - multivalued: false - range: float - ph_meth: - name: ph_meth - description: Reference or method used in determining pH - title: pH method + - equipment + - farm + slot_uri: MIXS:0001123 + multivalued: true + range: string + required: false + recommended: false + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + farm_water_source: + name: farm_water_source + description: Source of water used on the farm for irrigation of crops or watering + of livestock + title: farm watering water source examples: - - value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf + - value: well + description: was water well (ENVO:01000002) from_schema: https://w3id.org/mixs-6-2-rc keywords: - - method - - ph - slot_uri: MIXS:0001106 + - farm + - source + - water + slot_uri: MIXS:0001110 + range: FARM_WATER_SOURCE_ENUM + recommended: true + feat_pred: + name: feat_pred + description: Method used to predict UViGs features such as ORFs, integration site, + etc + title: feature prediction + examples: + - value: Prodigal;2.6.3;default parameters + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - feature + - predict + slot_uri: MIXS:0000061 multivalued: false range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ + syntax: ^{software};{version};{parameters}$ interpolated: true partial_match: true - ph_regm: - name: ph_regm - description: Information about treatment involving exposure of plants to varying - levels of ph of the growth media, treatment regimen including how many times - the treatment was repeated, how long each treatment lasted, and the start and - end time of the entire treatment; can include multiple regimen - title: pH regimen + ferm_chem_add: + name: ferm_chem_add + annotations: + Expected_value: + tag: Expected_value + value: chemical ingredient + description: Any chemicals that are added to the fermentation process to achieve + the desired final product + title: fermentation chemical additives examples: - - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M + - value: salt from_schema: https://w3id.org/mixs-6-2-rc keywords: - - ph - - regimen - slot_uri: MIXS:0001056 + - fermentation + string_serialization: '{float} {unit}' + slot_uri: MIXS:0001185 multivalued: true - range: string - phaeopigments: - name: phaeopigments + recommended: true + ferm_chem_add_perc: + name: ferm_chem_add_perc annotations: - Expected_value: - tag: Expected_value - value: phaeopigment name;measurement value Preferred_unit: tag: Preferred_unit - value: milligram per cubic meter - description: Concentration of phaeopigments; can include multiple phaeopigments - title: phaeopigments + value: percentage + description: The amount of chemical added to the fermentation process + title: fermentation chemical additives percentage examples: - - value: 2.5 milligram per cubic meter + - value: '0.01' from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000180 + keywords: + - fermentation + - percent + slot_uri: MIXS:0001186 multivalued: true - required: false - recommended: false - phosphate: - name: phosphate + range: float + recommended: true + ferm_headspace_oxy: + name: ferm_headspace_oxy annotations: Preferred_unit: tag: Preferred_unit - value: micromole per liter - description: Concentration of phosphate - title: phosphate + value: percentage + description: The amount of headspace oxygen in a fermentation vessel + title: fermentation headspace oxygen examples: - - value: 0.7 micromole per liter + - value: '0.05' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - phosphate - slot_uri: MIXS:0000505 + - fermentation + - oxygen + slot_uri: MIXS:0001187 + multivalued: false + range: float + recommended: true + ferm_medium: + name: ferm_medium + description: The growth medium used for the fermented food fermentation process, + which supplies the required nutrients. Usually this includes a carbon and nitrogen + source, water, micronutrients and chemical additives + title: fermentation medium + examples: + - value: molasses + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - fermentation + slot_uri: MIXS:0001188 multivalued: false range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - phosplipid_fatt_acid: - name: phosplipid_fatt_acid - annotations: - Expected_value: - tag: Expected_value - value: phospholipid fatty acid name;measurement value - description: Concentration of phospholipid fatty acids; can include multiple values - title: phospholipid fatty acid + recommended: true + ferm_pH: + name: ferm_pH + description: The pH of the fermented food fermentation process + title: fermentation pH examples: - - value: 2.98 milligram per liter + - value: '4.5' from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000181 - multivalued: true - required: false - recommended: false - photon_flux: - name: photon_flux + keywords: + - fermentation + - ph + slot_uri: MIXS:0001189 + multivalued: false + range: float + recommended: true + ferm_rel_humidity: + name: ferm_rel_humidity annotations: Preferred_unit: tag: Preferred_unit - value: number of photons per second per unit area - description: Measurement of photon flux - title: photon flux + value: percentage + description: The relative humidity of the fermented food fermentation process + title: fermentation relative humidity + comments: + - percent or float? examples: - - value: 3.926 micromole photons per second per square meter + - value: 95% from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000725 - multivalued: false + keywords: + - fermentation + - humidity + - relative + slot_uri: MIXS:0001190 range: string - required: false - recommended: false + recommended: true pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - photosynt_activ: - name: photosynt_activ + ferm_temp: + name: ferm_temp annotations: Preferred_unit: tag: Preferred_unit - value: mol m-2 s-1 - description: Measurement of photosythetic activity (i.e. leaf gas exchange / chlorophyll - fluorescence emissions / reflectance / transpiration) Please also include the - term method term detailing the method of activity measurement - title: photosynthetic activity + value: degree Celsius + description: The temperature of the fermented food fermentation process + title: fermentation temperature examples: - - value: 0.1 mol CO2 m-2 s-1 - description: added a magnitude to the example from the XLSX file, " mol CO2 - m-2 s-1" + - value: 22 degrees Celsius from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0001296 + keywords: + - fermentation + - temperature + slot_uri: MIXS:0001191 + multivalued: false range: string recommended: true pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? @@ -11736,264 +9743,289 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - photosynt_activ_meth: - name: photosynt_activ_meth - description: Reference or method used in measurement of photosythetic activity - title: photosynthetic activity method + ferm_time: + name: ferm_time + annotations: + Preferred_unit: + tag: Preferred_unit + value: days + description: The time duration of the fermented food fermentation process + title: fermentation time + examples: + - value: P10D from_schema: https://w3id.org/mixs-6-2-rc keywords: - - method - slot_uri: MIXS:0001336 - multivalued: true + - fermentation + - time + slot_uri: MIXS:0001192 + multivalued: false range: string recommended: true - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}|{text}$ + syntax: ^{duration}$ interpolated: true partial_match: true - plant_growth_med: - name: plant_growth_med - annotations: - Expected_value: - tag: Expected_value - value: EO or enumeration - description: Specification of the media for growing the plants or tissue cultured - samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in - vitro liquid culture medium. Recommended value is a specific value from EO:plant - growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) - or other controlled vocabulary - title: plant growth medium + ferm_vessel: + name: ferm_vessel + description: The type of vessel used for containment of the fermentation + title: fermentation vessel + examples: + - value: steel drum from_schema: https://w3id.org/mixs-6-2-rc keywords: - - growth - - plant - string_serialization: '{termLabel} [{termID}] or [husk|other artificial liquid - medium|other artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water]' - slot_uri: MIXS:0001057 + - fermentation + slot_uri: MIXS:0001193 + multivalued: false + range: string + recommended: true + fertilizer_admin: + name: fertilizer_admin + description: Type of fertilizer or amendment added to the soil or water for the + purpose of improving substrate health and quality for plant growth. This field + accepts terms listed under agronomic fertilizer (http://purl.obolibrary.org/obo/AGRO_00002062). + Multiple terms may apply and can be separated by pipes, listing in reverse chronological + order + title: fertilizer administration + examples: + - value: fish emulsion [AGRO:00000082] + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - administration + slot_uri: MIXS:0001127 multivalued: false + range: string required: false recommended: false - plant_part_maturity: - name: plant_part_maturity - annotations: - Expected_value: - tag: Expected_value - value: FOODON:03530050 - description: A description of the stage of development of a plant or plant part - based on maturity or ripeness. This field accepts terms listed under degree - of plant maturity (http://purl.obolibrary.org/obo/FOODON_03530050) - title: degree of plant part maturity + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + fertilizer_date: + name: fertilizer_date + description: Date of administration of soil amendment or fertilizer. Multiple + terms may apply and can be separated by pipes, listing in reverse chronological + order + title: fertilizer administration date examples: - - value: ripe or mature [FOODON:03530052] + - value: '2018-05-11T10:00:00+01:00' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - degree - - plant - string_serialization: '{term label}{term ID}' - slot_uri: MIXS:0001120 + - administration + - date + slot_uri: MIXS:0001128 multivalued: false + range: datetime required: false recommended: false - plant_product: - name: plant_product + fertilizer_regm: + name: fertilizer_regm annotations: Expected_value: tag: Expected_value - value: product name - description: Substance produced by the plant, where the sample was obtained from - title: plant product + value: fertilizer name;fertilizer amount;treatment interval and duration + Preferred_unit: + tag: Preferred_unit + value: gram, mole per liter, milligram per liter + description: Information about treatment involving the use of fertilizers; should + include the name of fertilizer, amount administered, treatment regimen including + how many times the treatment was repeated, how long each treatment lasted, and + the start and end time of the entire treatment; can include multiple fertilizer + regimens + title: fertilizer regimen examples: - - value: xylem sap [PO:0025539] + - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc keywords: - - plant - - product - string_serialization: '{text}' - slot_uri: MIXS:0001058 + - regimen + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000556 + multivalued: true + required: false + recommended: false + field: + name: field + description: Name of the hydrocarbon field (e.g. Albacora) + title: field name + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000291 multivalued: false - plant_reprod_crop: - name: plant_reprod_crop - description: Plant reproductive part used in the field during planting to start - the crop - title: plant reproductive part + range: string + recommended: true + filter_type: + name: filter_type + description: A device which removes solid particulates or airborne molecular contaminants + title: filter type examples: - - value: seedling + - value: HEPA from_schema: https://w3id.org/mixs-6-2-rc keywords: - - plant - slot_uri: MIXS:0001150 + - filter + - type + slot_uri: MIXS:0000765 multivalued: true - range: PLANT_REPROD_CROP_ENUM - required: false - recommended: false - plant_sex: - name: plant_sex - description: Sex of the reproductive parts on the whole plant, e.g. pistillate, - staminate, monoecieous, hermaphrodite - title: plant sex + range: FILTER_TYPE_ENUM + required: true + fire: + name: fire + description: Historical and/or physical evidence of fire + title: history/fire + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - history + slot_uri: MIXS:0001086 + multivalued: false + range: datetime + fireplace_type: + name: fireplace_type + description: A firebox with chimney + title: fireplace type examples: - - value: Hermaphroditic + - value: wood burning from_schema: https://w3id.org/mixs-6-2-rc keywords: - - plant - slot_uri: MIXS:0001059 + - type + slot_uri: MIXS:0000802 multivalued: false - range: PLANT_SEX_ENUM + range: FIREPLACE_TYPE_ENUM required: false recommended: false - plant_struc: - name: plant_struc - description: Name of plant structure the sample was obtained from; for Plant Ontology - (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, - e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the - sex of it can be recorded here - title: plant structure - examples: - - value: epidermis [PO:0005679] + flooding: + name: flooding + description: Historical and/or physical evidence of flooding + title: history/flooding from_schema: https://w3id.org/mixs-6-2-rc keywords: - - plant - slot_uri: MIXS:0001060 + - history + slot_uri: MIXS:0000319 + multivalued: false + range: datetime + floor_age: + name: floor_age + annotations: + Preferred_unit: + tag: Preferred_unit + value: years, weeks, days + description: The time period since installment of the carpet or flooring + title: floor age + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - age + - floor + slot_uri: MIXS:0000164 multivalued: false range: string - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - plant_water_method: - name: plant_water_method - description: Description of the equipment or method used to distribute water to - crops. This field accepts termed listed under irrigation process (http://purl.obolibrary.org/obo/AGRO_00000006). - Multiple terms can be separated by pipes - title: plant water delivery method - examples: - - value: drip irrigation process [AGRO:00000056] + floor_area: + name: floor_area + annotations: + Preferred_unit: + tag: Preferred_unit + value: square meter + description: The area of the floor space within the room + title: floor area from_schema: https://w3id.org/mixs-6-2-rc keywords: - - delivery - - method - - plant - - water - slot_uri: MIXS:0001111 + - area + - floor + slot_uri: MIXS:0000165 multivalued: false range: string - recommended: true - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - ploidy: - name: ploidy - description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, - triploid, tetraploid). It has implications for the downstream study of duplicated - gene and regions of the genomes (and perhaps for difficulties in assembly). - For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic - Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer - to http://purl.bioontology.org/ontology/PATO - title: ploidy + floor_cond: + name: floor_cond + description: The physical condition of the floor at the time of sampling; photos + or video preferred; use drawings to indicate location of damaged areas + title: floor condition examples: - - value: allopolyploidy [PATO:0001379] - in_subset: - - nucleic acid sequence source + - value: new from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000021 + keywords: + - condition + - floor + slot_uri: MIXS:0000803 multivalued: false - range: string - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ - structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ - interpolated: true - partial_match: true - pollutants: - name: pollutants - annotations: - Expected_value: - tag: Expected_value - value: pollutant name;measurement value - Preferred_unit: - tag: Preferred_unit - value: gram, mole per liter, milligram per liter, microgram per cubic meter - description: Pollutant types and, amount or concentrations measured at the time - of sampling; can report multiple pollutants by entering numeric values preceded - by name of pollutant - title: pollutants - examples: - - value: lead;0.15 microgram per cubic meter - from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000107 - multivalued: true + range: SHARED_ENUM_3 required: false recommended: false - pool_dna_extracts: - name: pool_dna_extracts - annotations: - Expected_value: - tag: Expected_value - value: pooling status;number of pooled extracts - Preferred_unit: - tag: Preferred_unit - value: gram, milliliter, microliter - description: Indicate whether multiple DNA extractions were mixed. If the answer - yes, the number of extracts that were pooled should be given - title: pooling of DNA extracts (if done) - examples: - - value: yes, 5 + floor_count: + name: floor_count + description: The number of floors in the building, including basements and mechanical + penthouse + title: floor count from_schema: https://w3id.org/mixs-6-2-rc keywords: - - dna - - pooling - slot_uri: MIXS:0000325 + - count + - floor + slot_uri: MIXS:0000225 multivalued: false - porosity: - name: porosity + range: integer + required: false + recommended: false + floor_finish_mat: + name: floor_finish_mat annotations: Expected_value: tag: Expected_value - value: measurement value or range - Preferred_unit: - tag: Preferred_unit - value: percentage - description: Porosity of deposited sediment is volume of voids divided by the - total volume of sample - title: porosity + value: enumeration + description: The floor covering type; the finished surface that is walked on + title: floor finish material + examples: + - value: carpet from_schema: https://w3id.org/mixs-6-2-rc keywords: - - porosity - string_serialization: '{float} - {float} {unit}' - slot_uri: MIXS:0000211 + - floor + - material + string_serialization: '[tile|wood strip or parquet|carpet|rug|laminate wood|lineoleum|vinyl + composition tile|sheet vinyl|stone|bamboo|cork|terrazo|concrete|none;specify + unfinished|sealed|clear finish|paint]' + slot_uri: MIXS:0000804 multivalued: false required: false recommended: false - pos_cont_type: - name: pos_cont_type - description: The substance, mixture, product, or apparatus used to verify that - a process which is part of an investigation delivers a true positive - title: positive control type - in_subset: - - investigation + floor_struc: + name: floor_struc + description: Refers to the structural elements and subfloor upon which the finish + flooring is installed + title: floor structure + examples: + - value: concrete from_schema: https://w3id.org/mixs-6-2-rc keywords: - - type - string_serialization: '{term} or {text}' - slot_uri: MIXS:0001322 + - floor + slot_uri: MIXS:0000806 multivalued: false - recommended: true - potassium: - name: potassium + range: FLOOR_STRUC_ENUM + required: false + recommended: false + floor_thermal_mass: + name: floor_thermal_mass annotations: Preferred_unit: tag: Preferred_unit - value: milligram per liter, parts per million - description: Concentration of potassium in the sample - title: potassium - examples: - - value: 463 milligram per liter + value: joule per degree Celsius + description: The ability of the floor to provide inertia against temperature fluctuations + title: floor thermal mass from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000430 + keywords: + - floor + - mass + slot_uri: MIXS:0000166 multivalued: false range: string required: false @@ -12004,19 +10036,32 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - pour_point: - name: pour_point + floor_water_mold: + name: floor_water_mold + description: Signs of the presence of mold or mildew in a room + title: floor signs of water/mold + examples: + - value: ceiling discoloration + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - floor + slot_uri: MIXS:0000805 + multivalued: false + range: FLOOR_WATER_MOLD_ENUM + required: false + recommended: false + fluor: + name: fluor annotations: Preferred_unit: tag: Preferred_unit - value: degree Celsius - description: 'Temperature at which a liquid becomes semi solid and loses its flow - characteristics. In crude oil a high pour point is generally associated with - a high paraffin content, typically found in crude deriving from a larger proportion - of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)' - title: pour point + value: milligram chlorophyll a per cubic meter, volts + description: Raw or converted fluorescence of water + title: fluorescence + examples: + - value: 2.5 volts from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000127 + slot_uri: MIXS:0000704 multivalued: false range: string required: false @@ -12027,622 +10072,547 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - pre_treatment: - name: pre_treatment - annotations: - Expected_value: - tag: Expected_value - value: pre-treatment type - description: The process of pre-treatment removes materials that can be easily - collected from the raw wastewater - title: pre-treatment + foetal_health_stat: + name: foetal_health_stat + description: Specification of foetal health status, should also include abortion + title: amniotic fluid/foetal health status from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text}' - slot_uri: MIXS:0000348 + keywords: + - status + slot_uri: MIXS:0000275 multivalued: false + range: string required: false recommended: false - pred_genome_struc: - name: pred_genome_struc - description: Expected structure of the viral genome - title: predicted genome structure - examples: - - value: non-segmented - in_subset: - - sequencing - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - predict - slot_uri: MIXS:0000083 - multivalued: false - range: PRED_GENOME_STRUC_ENUM - pred_genome_type: - name: pred_genome_type + food_additive: + name: food_additive annotations: Expected_value: tag: Expected_value - value: enumeration - description: Type of genome predicted for the UViG - title: predicted genome type + value: FOODON:03412972 + description: A substance or substances added to food to maintain or improve safety + and freshness, to improve or maintain nutritional value, or improve taste, texture + and appearance. This field accepts terms listed under food additive (http://purl.obolibrary.org/obo/FOODON_03412972). + Multiple terms can be separated by one or more pipes, but please consider limiting + this list to the top 5 ingredients listed in order as on the food label. See + also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors + title: food additive examples: - - value: dsDNA - in_subset: - - sequencing + - value: xanthan gum [FOODON:03413321] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - predict - - type - string_serialization: '[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (-)|mixed|uncharacterized]' - slot_uri: MIXS:0000082 - multivalued: false - pregnancy: - name: pregnancy - description: Date due of pregnancy - title: pregnancy - examples: - - value: '2013-03-25T12:42:31+01:00' - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000966 - multivalued: false - range: datetime + - food + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001200 + multivalued: true required: false recommended: false - pres_animal_insect: - name: pres_animal_insect + food_allergen_label: + name: food_allergen_label annotations: Expected_value: tag: Expected_value - value: enumeration;count - description: The type and number of animals or insects present in the sampling - space - title: presence of pets, animals, or insects + value: FOODON:03510213 + description: A label indication that the product contains a recognized allergen. + This field accepts terms listed under dietary claim or use (http://purl.obolibrary.org/obo/FOODON_03510213) + title: food allergen labeling examples: - - value: cat;5 + - value: food allergen labelling about crustaceans and products thereof [FOODON:03510215] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - animal - - presence - string_serialization: '[cat|dog|rodent|snake|other];{integer}' - slot_uri: MIXS:0000819 - multivalued: false + - food + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001201 + multivalued: true required: false recommended: false - pressure: - name: pressure - annotations: - Preferred_unit: - tag: Preferred_unit - value: atmosphere - description: Pressure to which the sample is subject to, in atmospheres - title: pressure + food_clean_proc: + name: food_clean_proc + description: The process of cleaning food to separate other environmental materials + from the food source. Multiple terms can be separated by pipes + title: food cleaning process examples: - - value: 50 atmosphere + - value: rinsed with water + description: was rinsed with water|scrubbed with brush + - value: scrubbed with brush + description: was rinsed with water|scrubbed with brush from_schema: https://w3id.org/mixs-6-2-rc keywords: - - pressure - slot_uri: MIXS:0000412 - multivalued: false - range: string + - food + - process + slot_uri: MIXS:0001182 + range: FOOD_CLEAN_PROC_ENUM required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - prev_land_use_meth: - name: prev_land_use_meth - description: Reference or method used in determining previous land use and dates - title: history/previous land use method + food_contact_surf: + name: food_contact_surf + annotations: + Expected_value: + tag: Expected_value + value: FOODON:03500010 + description: The specific container or coating materials in direct contact with + the food. Multiple values can be assigned. This field accepts terms listed + under food contact surface (http://purl.obolibrary.org/obo/FOODON_03500010) + title: food contact surface + examples: + - value: cellulose acetate [FOODON:03500034] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - history - - land - - method - - use - slot_uri: MIXS:0000316 - multivalued: false - range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ - structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ - interpolated: true - partial_match: true - previous_land_use: - name: previous_land_use + - food + - surface + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001131 + multivalued: true + food_contain_wrap: + name: food_contain_wrap annotations: Expected_value: tag: Expected_value - value: land use name;date - description: Previous land use and dates - title: history/previous land use + value: FOODON:03490100 + description: Type of container or wrapping defined by the main container material, + the container form, and the material of the liner lids or ends. Also type of + container or wrapping by form; prefer description by material first, then by + form. This field accepts terms listed under food container or wrapping (http://purl.obolibrary.org/obo/FOODON_03490100) + title: food container or wrapping examples: - - value: fallow; 2018-05-11:T14:30Z + - value: Plastic shrink-pack [FOODON:03490137] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - history - - land - - use - string_serialization: '{text};{timestamp}' - slot_uri: MIXS:0000315 + - food + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001132 multivalued: false - primary_prod: - name: primary_prod + required: false + recommended: false + food_cooking_proc: + name: food_cooking_proc annotations: - Preferred_unit: - tag: Preferred_unit - value: milligram per cubic meter per day, gram per square meter per day - description: Measurement of primary production, generally measured as isotope - uptake - title: primary production + Expected_value: + tag: Expected_value + value: FOODON:03450002 + description: The transformation of raw food by the application of heat. This field + accepts terms listed under food cooking (http://purl.obolibrary.org/obo/FOODON_03450002) + title: food cooking process examples: - - value: 100 milligram per cubic meter per day + - value: food blanching [FOODON:03470175] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - primary - - production - slot_uri: MIXS:0000728 - multivalued: false + - food + - process + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001202 + multivalued: true + required: false + recommended: false + food_dis_point: + name: food_dis_point + description: 'A reference to a place on the Earth, by its name or by its geographical + location that refers to a distribution point along the food chain. This field + accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448). + Reference: Adam Diamond, James Barham. Moving Food Along the Value Chain: Innovations + in Regional Food Distribution. U.S. Dept. of Agriculture, Agricultural Marketing + Service. Washington, DC. March 2012. http://dx.doi.org/10.9752/MS045.03-2012' + title: food distribution point geographic location + examples: + - value: 'USA: Delmarva, Peninsula' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - food + - geographic + - location + slot_uri: MIXS:0001203 + multivalued: true range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$' structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: '^{text}: {text}, {text}$' interpolated: true partial_match: true - primary_treatment: - name: primary_treatment + food_dis_point_city: + name: food_dis_point_city annotations: Expected_value: tag: Expected_value - value: primary treatment type - description: The process to produce both a generally homogeneous liquid capable - of being treated biologically and a sludge that can be separately treated or - processed - title: primary treatment + value: GAZ:00000448 + description: 'A reference to a place on the Earth, by its name or by its geographical + location that refers to a distribution point along the food chain. This field + accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448). + Reference: Adam Diamond, James Barham. Moving Food Along the Value Chain: Innovations + in Regional Food Distribution. U.S. Dept. of Agriculture, Agricultural Marketing + Service. Washington, DC. March 2012. http://dx.doi.org/10.9752/MS045.03-2012' + title: food distribution point geographic location (city) + examples: + - value: Atlanta[GAZ:00004445] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - primary - - treatment - string_serialization: '{text}' - slot_uri: MIXS:0000349 - multivalued: false + - food + - geographic + - location + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001204 + multivalued: true required: false recommended: false - prod_label_claims: - name: prod_label_claims - description: Labeling claims containing descriptors such as wild caught, free-range, - organic, free-range, industrial, hormone-free, antibiotic free, cage free. Can - include more than one term, separated by ";" - title: production labeling claims + food_harvest_proc: + name: food_harvest_proc + description: A harvesting process is a process which takes in some food material + from an individual or community of plant or animal organisms in a given context + and time, and outputs a precursor or consumable food product. This may include + a part of an organism or the whole, and may involve killing the organism + title: Food harvesting process examples: - - value: free range + - value: hand-picked from_schema: https://w3id.org/mixs-6-2-rc keywords: - - production - slot_uri: MIXS:prod_label_claims + - food + - process + slot_uri: MIXS:0001133 multivalued: true range: string required: false recommended: false - prod_rate: - name: prod_rate + food_ingredient: + name: food_ingredient annotations: - Preferred_unit: - tag: Preferred_unit - value: cubic meter per day - description: Oil and/or gas production rates per well (e.g. 524 m3 / day) - title: production rate + Expected_value: + tag: Expected_value + value: FOODON + description: In this field, please list individual ingredients for multi-component + food [FOODON:00002501] and simple foods that is not captured in food_type. Please + use terms that are present in FoodOn. Multiple terms can be separated by one + or more pipes |, but please consider limiting this list to the top 5 ingredients + listed in order as on the food label. See also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors + title: food ingredient + examples: + - value: bean (whole) [FOODON:00002753] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - production - - rate - slot_uri: MIXS:0000452 + - food + - ingredient + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001205 + multivalued: true + required: false + recommended: false + food_name_status: + name: food_name_status + description: A datum indicating that use of a food product name is regulated in + some legal jurisdiction. This field accepts terms listed under food product + name legal status (http://purl.obolibrary.org/obo/FOODON_03530087) + title: food product name legal status + examples: + - value: protected geographic indication [FOODON:03530256] + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - food + - product + - status + slot_uri: MIXS:0001206 multivalued: false range: string - recommended: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + required: false + recommended: false + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: ^{termLabel} \[{termID}\]$ interpolated: true partial_match: true - prod_start_date: - name: prod_start_date - description: Date of field's first production - title: production start date + food_origin: + name: food_origin + description: A reference to a place on the Earth, by its name or by its geographical + location that describes the origin of the food commodity, either in terms of + its cultivation or production. This field accepts terms listed under geographic + location (http://purl.obolibrary.org/obo/GAZ_00000448) + title: food product origin geographic location examples: - - value: '2013-03-25T12:42:31+01:00' + - value: 'USA: Delmarva, Peninsula' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - date - - production - - start - slot_uri: MIXS:0001008 + - food + - geographic + - location + - product + slot_uri: MIXS:0001207 multivalued: false - range: datetime - recommended: true - profile_position: - name: profile_position - description: Cross-sectional position in the hillslope where sample was collected.sample - area position in relation to surrounding areas - title: profile position - examples: - - value: summit - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0001084 - multivalued: false - range: PROFILE_POSITION_ENUM - project_name: - name: project_name - description: Name of the project within which the sequencing was organized - title: project name + range: string + pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$' + structured_pattern: + syntax: '^{text}: {text}, {text}$' + interpolated: true + partial_match: true + food_pack_capacity: + name: food_pack_capacity + annotations: + Preferred_unit: + tag: Preferred_unit + value: grams + description: The maximum number of product units within a package + title: food package capacity examples: - - value: Forest soil metagenome - in_subset: - - investigation + - value: 454 grams from_schema: https://w3id.org/mixs-6-2-rc keywords: - - project - slot_uri: MIXS:0000092 + - food + - package + slot_uri: MIXS:0001208 multivalued: false range: string - required: true - propagation: - name: propagation + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + food_pack_integrity: + name: food_pack_integrity annotations: Expected_value: tag: Expected_value - value: 'for virus: lytic, lysogenic, temperate, obligately lytic; for plasmid: - incompatibility group; for eukaryote: asexual, sexual; other more specific - values (e.g., incompatibility group) are allowed' - description: 'The type of reproduction from the parent stock. Values for this - field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately - lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual' - title: propagation + value: FOODON:03530218 + description: A term label and term id to describe the state of the packing material + and text to explain the exact condition. This field accepts terms listed under + food packing medium integrity (http://purl.obolibrary.org/obo/FOODON_03530218) + title: food packing medium integrity examples: - - value: lytic - in_subset: - - nucleic acid sequence source - from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text}' - slot_uri: MIXS:0000033 - multivalued: false - pulmonary_disord: - name: pulmonary_disord - description: History of pulmonary disorders; can include multiple disorders. The - terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - lung disease (https://disease-ontology.org/?id=DOID:850) - title: lung/pulmonary disorder + - value: food packing medium compromised [FOODON:00002517] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - disorder - slot_uri: MIXS:0000269 + - food + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001209 multivalued: true - range: string - required: false - recommended: false - quad_pos: - name: quad_pos - description: The quadrant position of the sampling room within the building - title: quadrant position - examples: - - value: West side - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000820 - multivalued: false - range: QUAD_POS_ENUM required: false recommended: false - radiation_regm: - name: radiation_regm + food_pack_medium: + name: food_pack_medium annotations: Expected_value: tag: Expected_value - value: radiation type name;radiation amount;treatment interval and duration - Preferred_unit: - tag: Preferred_unit - value: rad, gray - description: Information about treatment involving exposure of plant or a plant - part to a particular radiation regimen; should include the radiation type, amount - or intensity administered, treatment regimen including how many times the treatment - was repeated, how long each treatment lasted, and the start and end time of - the entire treatment; can include multiple radiation regimens - title: radiation regimen - examples: - - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + value: FOODON:03480020 + description: The medium in which the food is packed for preservation and handling + or the medium surrounding homemade foods, e.g., peaches cooked in sugar syrup. + The packing medium may provide a controlled environment for the food. It may + also serve to improve palatability and consumer appeal. This includes edible + packing media (e.g. fruit juice), gas other than air (e.g. carbon dioxide), + vacuum packed, or packed with aerosol propellant. This field accepts terms under + food packing medium (http://purl.obolibrary.org/obo/FOODON_03480020). Multiple + terms may apply and can be separated by pipes + title: food packing medium from_schema: https://w3id.org/mixs-6-2-rc keywords: - - regimen - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000575 + - food + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001134 multivalued: true required: false recommended: false - rainfall_regm: - name: rainfall_regm + food_preserv_proc: + name: food_preserv_proc annotations: Expected_value: tag: Expected_value - value: measurement value;treatment interval and duration - Preferred_unit: - tag: Preferred_unit - value: millimeter - description: Information about treatment involving an exposure to a given amount - of rainfall, treatment regimen including how many times the treatment was repeated, - how long each treatment lasted, and the start and end time of the entire treatment; - can include multiple regimens - title: rainfall regimen + value: FOODON:03470107 + description: The methods contributing to the prevention or retardation of microbial, + enzymatic or oxidative spoilage and thus to the extension of shelf life. This + field accepts terms listed under food preservation process (http://purl.obolibrary.org/obo/FOODON_03470107) + title: food preservation process examples: - - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: food slow freezing [FOODON:03470128] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - rain - - regimen - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' - slot_uri: MIXS:0000576 + - food + - process + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001135 multivalued: true required: false recommended: false - reactor_type: - name: reactor_type + food_prior_contact: + name: food_prior_contact annotations: Expected_value: tag: Expected_value - value: reactor type name - description: Anaerobic digesters can be designed and engineered to operate using - a number of different process configurations, as batch or continuous, mesophilic, - high solid or low solid, and single stage or multistage - title: reactor type + value: FOODON:03530077 + description: The material the food contacted (e.g., was processed in) prior to + packaging. This field accepts terms listed under material of contact prior to + food packaging (http://purl.obolibrary.org/obo/FOODON_03530077). If the proper + descriptor is not listed please use text to describe the material of contact + prior to food packaging + title: material of contact prior to food packaging + examples: + - value: processed in stainless steel container [FOODON:03530081] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - type - string_serialization: '{text}' - slot_uri: MIXS:0000350 - multivalued: false + - food + - material + - prior + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001210 + multivalued: true required: false recommended: false - reassembly_bin: - name: reassembly_bin - description: Has an assembly been performed on a genome bin extracted from a metagenomic - assembly? - title: reassembly post binning + food_prod: + name: food_prod + description: Descriptors of the food production system or of the agricultural + environment and growing conditions related to the farm production system, such + as wild caught, organic, free-range, industrial, dairy, beef, domestic or cultivated + food production. This field accepts terms listed under food production (http://purl.obolibrary.org/obo/FOODON_03530206). + Multiple terms may apply and can be separated by pipes + title: food production system characteristics examples: - - value: 'no' - in_subset: - - sequencing + - value: organic plant cultivation [FOODON:03530253] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - post - slot_uri: MIXS:0000079 - multivalued: false - range: boolean - redox_potential: - name: redox_potential - annotations: - Preferred_unit: - tag: Preferred_unit - value: millivolt - description: Redox potential, measured relative to a hydrogen cell, indicating - oxidation or reduction potential - title: redox potential - examples: - - value: 300 millivolt - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000182 - multivalued: false + - food + - production + slot_uri: MIXS:0001211 + multivalued: true range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: ^{termLabel} \[{termID}\]$ interpolated: true partial_match: true - ref_biomaterial: - name: ref_biomaterial - description: Primary publication if isolated before genome publication; otherwise, - primary genome report - title: reference for biomaterial + food_prod_char: + name: food_prod_char + description: Descriptors of the food production system such as wild caught, free-range, + organic, free-range, industrial, dairy, beef + title: food production characteristics examples: - - value: doi:10.1016/j.syapm.2018.01.009 - in_subset: - - nucleic acid sequence source + - value: wild caught from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000025 - multivalued: false + keywords: + - food + - production + slot_uri: MIXS:0001136 + multivalued: true range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ - structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ - interpolated: true - partial_match: true - ref_db: - name: ref_db - annotations: - Expected_value: - tag: Expected_value - value: names, versions, and references of databases - description: List of database(s) used for ORF annotation, along with version number - and reference to website or publication - title: reference database(s) - examples: - - value: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 - doi:10.1093/nar/gkw975 - in_subset: - - sequencing - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - database - string_serialization: '{database};{version};{reference}' - slot_uri: MIXS:0000062 - multivalued: false - rel_air_humidity: - name: rel_air_humidity - annotations: - Preferred_unit: - tag: Preferred_unit - value: percentage - description: Partial vapor and air pressure, density of the vapor and air, or - by the actual mass of the vapor and air - title: relative air humidity - comments: - - percent or float? + required: false + recommended: false + food_prod_synonym: + name: food_prod_synonym + description: Other names by which the food product is known by (e.g., regional + or non-English names) + title: food product synonym examples: - - value: '0.8' + - value: pinot gris from_schema: https://w3id.org/mixs-6-2-rc keywords: - - air - - humidity - - relative - slot_uri: MIXS:0000121 - range: float - required: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - rel_humidity_out: - name: rel_humidity_out - annotations: - Preferred_unit: - tag: Preferred_unit - value: gram of air, kilogram of air - description: The recorded outside relative humidity value at the time of sampling - title: outside relative humidity + - food + - product + slot_uri: MIXS:0001212 + multivalued: true + range: string + required: false + recommended: false + food_product_qual: + name: food_product_qual + description: Descriptors for describing food visually or via other senses, which + is useful for tasks like food inspection where little prior knowledge of how + the food came to be is available. Some terms like "food (frozen)" are both a + quality descriptor and the output of a process. This field accepts terms listed + under food product by quality (http://purl.obolibrary.org/obo/FOODON_00002454) + title: food product by quality examples: - - value: 12 per kilogram of air + - value: raw [FOODON:03311126] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - humidity - - relative - slot_uri: MIXS:0000188 + - food + - product + - quality + slot_uri: MIXS:0001213 multivalued: false range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: ^{termLabel} \[{termID}\]$ interpolated: true partial_match: true - rel_location: - name: rel_location - description: Location of sampled soil to other parts of the farm e.g. under crop - plant, near irrigation ditch, from the dirt road - title: relative location of sample - examples: - - value: furrow + food_product_type: + name: food_product_type + annotations: + Expected_value: + tag: Expected_value + value: FOODON:00001002 or FOODON:03309997 + description: A food product type is a class of food products that is differentiated + by its food composition (e.g., single- or multi-ingredient), processing and/or + consumption characteristics. This does not include brand name products but it + may include generic food dish categories. This field accepts terms under food + product type (http://purl.obolibrary.org/obo/FOODON:03400361). For terms related + to food product for an animal, consult food product for animal (http://purl.obolibrary.org/obo/FOODON_03309997). + If the proper descriptor is not listed please use text to describe the food + type. Multiple terms can be separated by one or more pipes + title: food product type from_schema: https://w3id.org/mixs-6-2-rc keywords: - - location - - relative - - sample - slot_uri: MIXS:0001161 + - food + - product + - type + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001184 multivalued: false - range: string - rel_samp_loc: - name: rel_samp_loc - description: The sampling location within the train car - title: relative sampling location + food_quality_date: + name: food_quality_date + annotations: + Expected_value: + tag: Expected_value + value: enumeration, date + description: The date recommended for the use of the product while at peak quality, + this date is not a reflection of safety unless used on infant formula this date + is not a reflection of safety and is typically labeled on a food product as + "best if used by," best by," "use by," or "freeze by." + title: food quality date examples: - - value: center of car + - value: best by 2020-05-24 from_schema: https://w3id.org/mixs-6-2-rc keywords: - - location - - relative - slot_uri: MIXS:0000821 + - date + - food + - quality + string_serialization: '[best by|best if used by|freeze by|use by]; date' + slot_uri: MIXS:0001178 multivalued: false - range: REL_SAMP_LOC_ENUM required: false recommended: false - rel_to_oxygen: - name: rel_to_oxygen - description: Is this organism an aerobe, anaerobe? Please note that aerobic and - anaerobic are valid descriptors for microbial environments - title: relationship to oxygen - examples: - - value: aerobe - in_subset: - - nucleic acid sequence source - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - oxygen - - relationship - slot_uri: MIXS:0000015 - multivalued: false - range: REL_TO_OXYGEN_ENUM - repository_name: - name: repository_name + food_source: + name: food_source annotations: Expected_value: tag: Expected_value - value: Institution - description: The name of the institution where the sample or DNA extract is held - or "sample not available" if the sample was used in its entirety for analysis - or otherwise not retained - title: repository name - examples: - - value: FDA CFSAN Microbiology Laboratories - from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text}' - slot_uri: MIXS:0001152 - multivalued: true - required: false - recommended: false - reservoir: - name: reservoir - description: Name of the reservoir (e.g. Carapebus) - title: reservoir name - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000303 - multivalued: false - range: string - recommended: true - resins_pc: - name: resins_pc - annotations: - Preferred_unit: - tag: Preferred_unit - value: percent - description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis - method that divides crude oil components according to their polarizability - and polarity. There are three main methods to obtain SARA results. The most - popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: - https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' - title: resins wt% + value: FOODON term + description: Type of plant or animal from which the food product or its major + ingredient is derived or a chemical food source [FDA CFSAN 1995] + title: food source from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000134 + keywords: + - food + - source + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0001139 multivalued: false - range: string - recommended: true - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{name};{float} {unit}$ - interpolated: true - partial_match: true - room_air_exch_rate: - name: room_air_exch_rate + food_source_age: + name: food_source_age annotations: Preferred_unit: tag: Preferred_unit - value: liter per hour - description: The rate at which outside air replaces indoor air in a given space - title: room air exchange rate + value: days + description: The age of the food source host organim. Depending on the type of + host organism, age may be more appropriate to report in days, weeks, or years + title: food source age + comments: + - ISO 8601 period or measurement value? + examples: + - value: 6 months from_schema: https://w3id.org/mixs-6-2-rc keywords: - - air - - rate - - room - slot_uri: MIXS:0000169 - multivalued: false + - age + - food + - source + slot_uri: MIXS:0001251 range: string required: false recommended: false @@ -12652,1034 +10622,975 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - room_architec_elem: - name: room_architec_elem - description: The unique details and component parts that, together, form the architecture - of a distinguisahable space within a built structure - title: room architectural elements + food_trace_list: + name: food_trace_list + description: The FDA is proposing to establish additional traceability recordkeeping + requirements (beyond what is already required in existing regulations) for persons + who manufacture, process, pack, or hold foods the Agency has designated for + inclusion on the Food Traceability List. The Food Traceability List (FTL) identifies + the foods for which the additional traceability records described in the proposed + rule would be required. The term Food Traceability List (FTL) refers not only + to the foods specifically listed (https://www.fda.gov/media/142303/download), + but also to any foods that contain listed foods as ingredients + title: food traceability list category + examples: + - value: tropical tree fruits from_schema: https://w3id.org/mixs-6-2-rc keywords: - - room - slot_uri: MIXS:0000233 + - food + slot_uri: MIXS:0001214 multivalued: false - range: string + range: FOOD_TRACE_LIST_ENUM required: false recommended: false - room_condt: - name: room_condt - description: The condition of the room at the time of sampling - title: room condition + food_trav_mode: + name: food_trav_mode + description: A descriptor for the method of movement of food commodity along the + food distribution system. This field accepts terms listed under travel mode + (http://purl.obolibrary.org/obo/GENEPIO_0001064). If the proper descrptor is + not listed please use text to describe the mode of travel. Multiple terms can + be separated by one or more pipes + title: food shipping transportation method examples: - - value: new + - value: train travel [GENEPIO:0001060] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - condition - - room - slot_uri: MIXS:0000822 - multivalued: false - range: ROOM_CONDT_ENUM + - food + - method + - transport + slot_uri: MIXS:0001137 + multivalued: true + range: string required: false recommended: false - room_connected: - name: room_connected - description: List of rooms connected to the sampling room by a doorway - title: rooms connected by a doorway + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + food_trav_vehic: + name: food_trav_vehic + annotations: + Expected_value: + tag: Expected_value + value: ENVO:01000604 + description: A descriptor for the mobile machine which is used to transport food + commodities along the food distribution system. This field accepts terms listed + under vehicle (http://purl.obolibrary.org/obo/ENVO_01000604). If the proper + descrptor is not listed please use text to describe the mode of travel. Multiple + terms can be separated by one or more pipes + title: food shipping transportation vehicle examples: - - value: office - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - doorway - - room - slot_uri: MIXS:0000826 - multivalued: false - range: ROOM_CONNECTED_ENUM - required: false - recommended: false - room_count: - name: room_count - description: The total count of rooms in the built structure including all room - types - title: room count + - value: aircraft [ENVO:01001488]|car [ENVO:01000605] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - count - - room - slot_uri: MIXS:0000234 - multivalued: false - range: integer + - food + - transport + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001138 + multivalued: true required: false recommended: false - room_dim: - name: room_dim + food_treat_proc: + name: food_treat_proc annotations: Expected_value: tag: Expected_value - value: measurement value - Preferred_unit: - tag: Preferred_unit - value: meter - description: The length, width and height of sampling room - title: room dimensions + value: FOODON:03460111 + description: Used to specifically characterize a food product based on the treatment + or processes applied to the product or any indexed ingredient. The processes + include adding, substituting or removing components or modifying the food or + component, e.g., through fermentation. Multiple values can be assigned. This + fields accepts terms listed under food treatment process (http://purl.obolibrary.org/obo/FOODON_03460111) + title: food treatment process examples: - - value: 4 meter x 4 meter x 4 meter + - value: gluten removal process [FOODON:03460750] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - dimensions - - room - string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}' - slot_uri: MIXS:0000192 - multivalued: false + - food + - process + - treatment + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001140 + multivalued: true required: false recommended: false - room_door_dist: - name: room_door_dist - annotations: - Preferred_unit: - tag: Preferred_unit - value: meter - description: Distance between doors (meters) in the hallway between the sampling - room and adjacent rooms - title: room door distance + freq_clean: + name: freq_clean + description: The number of times the sample location is cleaned. Frequency of + cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually + title: frequency of cleaning + examples: + - value: Daily from_schema: https://w3id.org/mixs-6-2-rc keywords: - - distance - - door - - room - slot_uri: MIXS:0000193 + - frequency + slot_uri: MIXS:0000226 multivalued: false - range: string + range: FREQ_CLEAN_ENUM required: false recommended: false - pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{integer} {text}$ - interpolated: true - partial_match: true - room_door_share: - name: room_door_share - description: List of room(s) (room number, room name) sharing a door with the - sampling room - title: rooms that share a door with sampling room + freq_cook: + name: freq_cook + description: The number of times a meal is cooked per week + title: frequency of cooking from_schema: https://w3id.org/mixs-6-2-rc keywords: - - door - - room - slot_uri: MIXS:0000242 + - frequency + slot_uri: MIXS:0000227 multivalued: false range: string required: false recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{room_name};{room_number}$ + syntax: ^{integer} {text}$ interpolated: true partial_match: true - room_hallway: - name: room_hallway - description: List of room(s) (room number, room name) located in the same hallway - as sampling room - title: rooms that are on the same hallway + fungicide_regm: + name: fungicide_regm + annotations: + Preferred_unit: + tag: Preferred_unit + value: gram, mole per liter, milligram per liter + description: Information about treatment involving use of fungicides; should include + the name of fungicide, amount administered, treatment regimen including how + many times the treatment was repeated, how long each treatment lasted, and the + start and end time of the entire treatment; can include multiple fungicide regimens + title: fungicide regimen + examples: + - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc keywords: - - hallway - - room - slot_uri: MIXS:0000238 - multivalued: false + - regimen + slot_uri: MIXS:0000557 + multivalued: true range: string - required: false - recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ - structured_pattern: - syntax: ^{room_name};{room_number}$ - interpolated: true - partial_match: true - room_loc: - name: room_loc - description: The position of the room within the building - title: room location in building + furniture: + name: furniture + description: The types of furniture present in the sampled room + title: furniture examples: - - value: interior room - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - location - - room - slot_uri: MIXS:0000823 - multivalued: false - range: ROOM_LOC_ENUM - required: false - recommended: false - room_moist_dam_hist: - name: room_moist_dam_hist - description: The history of moisture damage or mold in the past 12 months. Number - of events of moisture damage or mold observed - title: room moisture damage or mold history + - value: chair from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - history - - moisture - - room - slot_uri: MIXS:0000235 + slot_uri: MIXS:0000807 multivalued: false - range: integer + range: FURNITURE_ENUM required: false recommended: false - room_net_area: - name: room_net_area + gaseous_environment: + name: gaseous_environment annotations: Preferred_unit: tag: Preferred_unit - value: square feet, square meter - description: The net floor area of sampling room. Net area excludes wall thicknesses - title: room net area + value: micromole per liter + description: Use of conditions with differing gaseous environments; should include + the name of gaseous compound, amount administered, treatment duration, interval + and total experimental duration; can include multiple gaseous environment regimens + title: gaseous environment + examples: + - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc keywords: - - area - - room - slot_uri: MIXS:0000194 - multivalued: false + - environment + slot_uri: MIXS:0000558 + multivalued: true range: string + gaseous_substances: + name: gaseous_substances + annotations: + Expected_value: + tag: Expected_value + value: gaseous substance name;measurement value + Preferred_unit: + tag: Preferred_unit + value: micromole per liter + description: Amount or concentration of substances such as hydrogen sulfide, carbon + dioxide, methane, etc.; can include multiple substances + title: gaseous substances + from_schema: https://w3id.org/mixs-6-2-rc + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000661 + multivalued: true required: false recommended: false - pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{integer} {text}$ - interpolated: true - partial_match: true - room_occup: - name: room_occup - description: Count of room occupancy at time of sampling - title: room occupancy + gastrointest_disord: + name: gastrointest_disord + description: History of gastrointestinal tract disorders; can include multiple + disorders. History of blood disorders; can include multiple disorders. The + terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77) + title: gastrointestinal tract disorder from_schema: https://w3id.org/mixs-6-2-rc keywords: - - room - slot_uri: MIXS:0000236 - multivalued: false + - disorder + slot_uri: MIXS:0000280 + multivalued: true range: string required: false recommended: false - pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{integer} {text}$ - interpolated: true - partial_match: true - room_samp_pos: - name: room_samp_pos - description: The horizontal sampling position in the room relative to architectural - elements - title: room sampling position + gender_restroom: + name: gender_restroom + description: The gender type of the restroom + title: gender of restroom examples: - - value: south corner + - value: male from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - room - slot_uri: MIXS:0000824 + slot_uri: MIXS:0000808 multivalued: false - range: ROOM_SAMP_POS_ENUM + range: GENDER_RESTROOM_ENUM required: false recommended: false - room_type: - name: room_type + genetic_mod: + name: genetic_mod annotations: Expected_value: tag: Expected_value - value: enumeration - description: The main purpose or activity of the sampling room. A room is any - distinguishable space within a structure - title: room type + value: PMID, DOI, URL or text + description: Genetic modifications of the genome of an organism, which may occur + naturally by spontaneous mutation, or be introduced by some experimental means, + e.g. specification of a transgene or the gene knocked-out or details of transient + transfection + title: genetic modification examples: - - value: bathroom + - value: aox1A transgenic from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - room - - type - string_serialization: '[attic|bathroom|closet|conference room|elevator|examining - room|hallway|kitchen|mail room|private office|open office|stairwell|,restroom|lobby|vestibule|mechanical - or electrical room|data center|laboratory_wet|laboratory_dry|gymnasium|natatorium|auditorium|lockers|cafe|warehouse]' - slot_uri: MIXS:0000825 + string_serialization: '{PMID}|{DOI}|{URL}' + slot_uri: MIXS:0000859 multivalued: false required: false recommended: false - room_vol: - name: room_vol - annotations: - Preferred_unit: - tag: Preferred_unit - value: cubic feet, cubic meter - description: Volume of sampling room - title: room volume + geo_loc_name: + name: geo_loc_name + description: The geographical origin of the sample as defined by the country or + sea name followed by specific region name. Country or sea names should be chosen + from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology + (http://purl.bioontology.org/ontology/GAZ) + title: geographic location (country and/or sea,region) + examples: + - value: 'USA: Maryland, Bethesda' + in_subset: + - environment from_schema: https://w3id.org/mixs-6-2-rc keywords: - - room - - volume - slot_uri: MIXS:0000195 + - geographic + - location + slot_uri: MIXS:0000010 multivalued: false range: string - required: false - recommended: false - pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + required: true + pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$' structured_pattern: - syntax: ^{integer} {text}$ + syntax: '^{text}: {text}, {text}$' interpolated: true partial_match: true - room_wall_share: - name: room_wall_share - description: List of room(s) (room number, room name) sharing a wall with the - sampling room - title: rooms that share a wall with sampling room + gestation_state: + name: gestation_state + description: Specification of the gestation state + title: amniotic fluid/gestation state from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - room - - wall - slot_uri: MIXS:0000243 + slot_uri: MIXS:0000272 multivalued: false range: string required: false recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ - structured_pattern: - syntax: ^{room_name};{room_number}$ - interpolated: true - partial_match: true - room_window_count: - name: room_window_count - description: Number of windows in the room - title: room window count - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - count - - room - - window - slot_uri: MIXS:0000237 - multivalued: false - range: integer - required: false - recommended: false - root_cond: - name: root_cond - description: Relevant rooting conditions such as field plot size, sowing density, - container dimensions, number of plants per container - title: rooting conditions + glucosidase_act: + name: glucosidase_act + annotations: + Preferred_unit: + tag: Preferred_unit + value: mol per liter per hour + description: Measurement of glucosidase activity + title: glucosidase activity examples: - - value: http://himedialabs.com/TD/PT158.pdf + - value: 5 mol per liter per hour from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - condition - slot_uri: MIXS:0001061 + slot_uri: MIXS:0000137 multivalued: false range: string required: false recommended: false - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}|{text}$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - root_med_carbon: - name: root_med_carbon - annotations: - Expected_value: - tag: Expected_value - value: carbon source name;measurement value - Preferred_unit: - tag: Preferred_unit - value: milligram per liter - description: Source of organic carbon in the culture rooting medium; e.g. sucrose - title: rooting medium carbon + gravidity: + name: gravidity + description: Whether or not subject is gravid, and if yes date due or date post-conception, + specifying which is used + title: gravidity examples: - - value: sucrose + - value: yes;due date:2018-05-11 from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - carbon - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000577 + string_serialization: '{boolean};{timestamp}' + slot_uri: MIXS:0000875 multivalued: false required: false recommended: false - root_med_macronutr: - name: root_med_macronutr + gravity: + name: gravity annotations: Expected_value: tag: Expected_value - value: macronutrient name;measurement value + value: gravity factor value;treatment interval and duration Preferred_unit: tag: Preferred_unit - value: milligram per liter - description: Measurement of the culture rooting medium macronutrients (N,P, K, - Ca, Mg, S); e.g. KH2PO4 (170 mg/L) - title: rooting medium macronutrients + value: meter per square second, g + description: Information about treatment involving use of gravity factor to study + various types of responses in presence, absence or modified levels of gravity; + treatment regimen including how many times the treatment was repeated, how long + each treatment lasted, and the start and end time of the entire treatment; can + include multiple treatments + title: gravity examples: - - value: KH2PO4;170 milligram per liter + - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - macronutrients - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000578 - multivalued: false + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000559 + multivalued: true required: false recommended: false - root_med_micronutr: - name: root_med_micronutr + growth_facil: + name: growth_facil annotations: Expected_value: tag: Expected_value - value: micronutrient name;measurement value - Preferred_unit: - tag: Preferred_unit - value: milligram per liter - description: Measurement of the culture rooting medium micronutrients (Fe, Mn, - Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L) - title: rooting medium micronutrients + value: free text or CO + description: 'Type of facility where the sampled plant was grown; controlled vocabulary: + growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively + use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research' + title: growth facility examples: - - value: H3BO3;6.2 milligram per liter + - value: Growth chamber [CO_715:0000189] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - micronutrients - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000579 + - facility + - growth + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001043 multivalued: false required: false recommended: false - root_med_ph: - name: root_med_ph - description: pH measurement of the culture rooting medium; e.g. 5.5 - title: rooting medium pH + growth_habit: + name: growth_habit + description: Characteristic shape, appearance or growth form of a plant species + title: growth habit examples: - - value: '7.5' + - value: spreading from_schema: https://w3id.org/mixs-6-2-rc keywords: - - ph - slot_uri: MIXS:0001062 + - growth + slot_uri: MIXS:0001044 multivalued: false - range: float + range: GROWTH_HABIT_ENUM required: false recommended: false - root_med_regl: - name: root_med_regl + growth_hormone_regm: + name: growth_hormone_regm annotations: Expected_value: tag: Expected_value - value: regulator name;measurement value + value: growth hormone name;growth hormone amount;treatment interval and duration Preferred_unit: tag: Preferred_unit - value: milligram per liter - description: Growth regulators in the culture rooting medium such as cytokinins, - auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA - title: rooting medium regulators + value: gram, mole per liter, milligram per liter + description: Information about treatment involving use of growth hormones; should + include the name of growth hormone, amount administered, treatment regimen including + how many times the treatment was repeated, how long each treatment lasted, and + the start and end time of the entire treatment; can include multiple growth + hormone regimens + title: growth hormone regimen examples: - - value: abscisic acid;0.75 milligram per liter + - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000581 - multivalued: false + keywords: + - growth + - regimen + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000560 + multivalued: true required: false recommended: false - root_med_solid: - name: root_med_solid - description: Specification of the solidifying agent in the culture rooting medium; - e.g. agar - title: rooting medium solidifier + growth_medium: + name: growth_medium + description: A liquid or gel containing nutrients, salts, and other factors formulated + to support the growth of microorganisms, cells, or plants (National Cancer Institute + Thesaurus). The name of the medium used to grow the microorganism + title: growth medium examples: - - value: agar + - value: LB broth from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0001063 + keywords: + - growth + slot_uri: MIXS:0001108 multivalued: false range: string required: false recommended: false - root_med_suppl: - name: root_med_suppl - annotations: - Expected_value: - tag: Expected_value - value: supplement name;measurement value - Preferred_unit: - tag: Preferred_unit - value: milligram per liter - description: Organic supplements of the culture rooting medium, such as vitamins, - amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid - (0.5 mg/L) - title: rooting medium organic supplements - examples: - - value: nicotinic acid;0.5 milligram per liter + gynecologic_disord: + name: gynecologic_disord + description: History of gynecological disorders; can include multiple disorders. + The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + female reproductive system disease (https://disease-ontology.org/?id=DOID:229) + title: gynecological disorder from_schema: https://w3id.org/mixs-6-2-rc keywords: - - organic - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000580 - multivalued: false + - disorder + slot_uri: MIXS:0000288 + multivalued: true + range: string required: false recommended: false - route_transmission: - name: route_transmission - description: Description of path taken by the symbiotic host organism being sampled - in order to establish a symbiotic relationship with the host (with which it - was observed at the time of sampling) via a mode of transmission (specified - in mode_transmission) - title: route of transmission + hall_count: + name: hall_count + description: The total count of hallways and cooridors in the built structure + title: hallway/corridor count from_schema: https://w3id.org/mixs-6-2-rc keywords: - - route - slot_uri: MIXS:0001316 + - corridor + - count + - hallway + slot_uri: MIXS:0000228 multivalued: false - range: ROUTE_TRANSMISSION_ENUM + range: integer required: false recommended: false - salinity: - name: salinity + handidness: + name: handidness + description: The handidness of the individual sampled + title: handidness + examples: + - value: right handedness + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000809 + multivalued: false + range: HANDIDNESS_ENUM + required: false + recommended: false + hc_produced: + name: hc_produced + description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, + etc). If "other" is specified, please propose entry in "additional info" field + title: hydrocarbon type produced + examples: + - value: Gas + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - hydrocarbon + - type + slot_uri: MIXS:0000989 + multivalued: false + range: HC_PRODUCED_ENUM + required: true + hcr: + name: hcr + description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR + defined as a natural environmental feature containing large amounts of hydrocarbons + at high concentrations potentially suitable for commercial exploitation. This + term should not be confused with the Hydrocarbon Occurrence term which also + includes hydrocarbon-rich environments with currently limited commercial interest + such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose + entry in "additional info" field + title: hydrocarbon resource type + examples: + - value: Oil Sand + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - hydrocarbon + - resource + - type + slot_uri: MIXS:0000988 + multivalued: false + range: HCR_ENUM + required: true + hcr_fw_salinity: + name: hcr_fw_salinity annotations: Preferred_unit: tag: Preferred_unit - value: practical salinity unit, percentage - description: The total concentration of all dissolved salts in a liquid or solid - sample. While salinity can be measured by a complete chemical analysis, this - method is difficult and time consuming. More often, it is instead derived from - the conductivity measurement. This is known as practical salinity. These derivations - compare the specific conductance of the sample to a salinity standard such as - seawater - title: salinity - examples: - - value: 25 practical salinity unit + value: milligram per liter + description: Original formation water salinity (prior to secondary recovery e.g. + Waterflooding) expressed as TDS + title: formation water salinity from_schema: https://w3id.org/mixs-6-2-rc keywords: - salinity - slot_uri: MIXS:0000183 + - water + slot_uri: MIXS:0000406 multivalued: false range: string - required: false - recommended: false + recommended: true pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - salt_regm: - name: salt_regm - annotations: - Preferred_unit: - tag: Preferred_unit - value: gram, microgram, mole per liter, gram per liter - description: Information about treatment involving use of salts as supplement - to liquid and soil growth media; should include the name of salt, amount administered, - treatment regimen including how many times the treatment was repeated, how long - each treatment lasted, and the start and end time of the entire treatment; can - include multiple salt regimens - title: salt regimen + hcr_geol_age: + name: hcr_geol_age + description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). + If "other" is specified, please propose entry in "additional info" field' + title: hydrocarbon resource geological age examples: - - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: Silurian from_schema: https://w3id.org/mixs-6-2-rc keywords: - - regimen - - salt - slot_uri: MIXS:0000582 - multivalued: true - range: string - samp_capt_status: - name: samp_capt_status - description: Reason for the sample - title: sample capture status - examples: - - value: farm sample + - age + - hydrocarbon + - resource + slot_uri: MIXS:0000993 + multivalued: false + range: SHARED_ENUM_5 + recommended: true + hcr_pressure: + name: hcr_pressure + annotations: + Preferred_unit: + tag: Preferred_unit + value: atmosphere, kilopascal + description: Original pressure of the hydrocarbon resource + title: hydrocarbon resource original pressure from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sample - - status - slot_uri: MIXS:0000860 + - hydrocarbon + - pressure + - resource + slot_uri: MIXS:0000395 multivalued: false - range: SAMP_CAPT_STATUS_ENUM + range: string required: false recommended: false - samp_collect_device: - name: samp_collect_device + pattern: ^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{float} *- *{float} {unit}$ + interpolated: true + partial_match: true + hcr_temp: + name: hcr_temp annotations: - Expected_value: - tag: Expected_value - value: device name - description: The device used to collect an environmental sample. This field accepts - terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). - This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094) - title: sample collection device - in_subset: - - nucleic acid sequence source - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - device - - sample - string_serialization: '{termLabel} [{termID}]|{text}' - slot_uri: MIXS:0000002 - multivalued: false - samp_collect_method: - name: samp_collect_method - description: The method employed for collecting the sample - title: sample collection method - in_subset: - - nucleic acid sequence source + Preferred_unit: + tag: Preferred_unit + value: degree Celsius + description: Original temperature of the hydrocarbon resource + title: hydrocarbon resource original temperature + examples: + - value: 150-295 degree Celsius from_schema: https://w3id.org/mixs-6-2-rc keywords: - - method - - sample - slot_uri: MIXS:0001225 + - hydrocarbon + - resource + - temperature + slot_uri: MIXS:0000393 multivalued: false range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}|{text}$ + syntax: ^{float} *- *{float} {unit}$ interpolated: true partial_match: true - samp_collect_point: - name: samp_collect_point - description: Sampling point on the asset were sample was collected (e.g. Wellhead, - storage tank, separator, etc). If "other" is specified, please propose entry - in "additional info" field - title: sample collection point + heat_cool_type: + name: heat_cool_type + description: Methods of conditioning or heating a room or building + title: heating and cooling system type examples: - - value: well + - value: heat pump from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sample - slot_uri: MIXS:0001015 - multivalued: false - range: SAMP_COLLECT_POINT_ENUM + - type + slot_uri: MIXS:0000766 + multivalued: true + range: HEAT_COOL_TYPE_ENUM required: true - samp_dis_stage: - name: samp_dis_stage - description: Stage of the disease at the time of sample collection, e.g. inoculation, - penetration, infection, growth and reproduction, dissemination of pathogen - title: sample disease stage + heat_deliv_loc: + name: heat_deliv_loc + description: The location of heat delivery within the room + title: heating delivery locations examples: - - value: infection + - value: north from_schema: https://w3id.org/mixs-6-2-rc keywords: - - disease - - sample - slot_uri: MIXS:0000249 + - delivery + - location + - locations + slot_uri: MIXS:0000810 multivalued: false - range: SAMP_DIS_STAGE_ENUM + range: SHARED_ENUM_0 required: false recommended: false - samp_floor: - name: samp_floor - annotations: - Expected_value: - tag: Expected_value - value: enumeration - description: The floor of the building, where the sampling room is located - title: sampling floor + heat_sys_deliv_meth: + name: heat_sys_deliv_meth + description: The method by which the heat is delivered through the system + title: heating system delivery method examples: - - value: 4th floor + - value: radiant from_schema: https://w3id.org/mixs-6-2-rc keywords: - - floor - string_serialization: '[1st floor|2nd floor|{integer} floor|basement|lobby]' - slot_uri: MIXS:0000828 + - delivery + - method + slot_uri: MIXS:0000812 multivalued: false + range: HEAT_SYS_DELIV_METH_ENUM required: false recommended: false - samp_loc_condition: - name: samp_loc_condition - description: The condition of the sample location at the time of sampling - title: sample location condition - examples: - - value: new + heat_system_id: + name: heat_system_id + description: The heating system identifier + title: heating system identifier from_schema: https://w3id.org/mixs-6-2-rc keywords: - - condition - - location - - sample - slot_uri: MIXS:0001257 + - identifier + slot_uri: MIXS:0000833 multivalued: false - range: SAMP_LOC_CONDITION_ENUM + range: integer required: false recommended: false - samp_loc_corr_rate: - name: samp_loc_corr_rate + heavy_metals: + name: heavy_metals annotations: + Expected_value: + tag: Expected_value + value: heavy metal name;measurement value unit Preferred_unit: tag: Preferred_unit - value: millimeter per year - description: Metal corrosion rate is the speed of metal deterioration due to environmental - conditions. As environmental conditions change corrosion rates change accordingly. - Therefore, long term corrosion rates are generally more informative than short - term rates and for that reason they are preferred during reporting. In the case - of suspected MIC, corrosion rate measurements at the time of sampling might - provide insights into the involvement of certain microbial community members - in MIC as well as potential microbial interplays - title: corrosion rate at sample location + value: microgram per gram + description: Heavy metals present in the sequenced sample and their concentrations. + For multiple heavy metals and concentrations, add multiple copies of this field + title: extreme_unusual_properties/heavy metals + examples: + - value: mercury;0.09 micrograms per gram from_schema: https://w3id.org/mixs-6-2-rc keywords: - - location - - rate - - sample - slot_uri: MIXS:0000136 + - extreme + - properties + - unusual + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000652 + multivalued: true + required: false + recommended: false + heavy_metals_meth: + name: heavy_metals_meth + description: Reference or method used in determining heavy metals + title: extreme_unusual_properties/heavy metals method + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - extreme + - method + - properties + - unusual + slot_uri: MIXS:0000343 multivalued: false range: string - recommended: true - pattern: ^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ structured_pattern: - syntax: ^{float} *- *{float} {unit}$ + syntax: ^{PMID}|{DOI}|{URL}$ interpolated: true partial_match: true - samp_mat_process: - name: samp_mat_process - description: A brief description of any processing applied to the sample during - or after retrieving the sample from environment, or a link to the relevant protocol(s) - performed - title: sample material processing - examples: - - value: filtering of seawater, storing samples in ethanol - in_subset: - - nucleic acid sequence source - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - material - - process - - sample - slot_uri: MIXS:0000016 - multivalued: false - range: string - samp_md: - name: samp_md + height_carper_fiber: + name: height_carper_fiber annotations: - Expected_value: - tag: Expected_value - value: measurement value;enumeration Preferred_unit: tag: Preferred_unit - value: meter - description: In non deviated well, measured depth is equal to the true vertical - depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated - wells, the MD is the length of trajectory of the borehole measured from the - same reference or datum. Common datums used are ground level (GL), drilling - rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). - If "other" is specified, please propose entry in "additional info" field - title: sample measured depth - examples: - - value: 1534 meter;MSL + value: centimeter + description: The average carpet fiber height in the indoor environment + title: height carpet fiber mat from_schema: https://w3id.org/mixs-6-2-rc keywords: - - depth - - measurement - - sample - string_serialization: '{float} {unit};[GL|DF|RT|KB|MSL|other]' - slot_uri: MIXS:0000413 + - height + slot_uri: MIXS:0000167 multivalued: false + range: string required: false recommended: false - samp_name: - name: samp_name + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + herbicide_regm: + name: herbicide_regm annotations: Preferred_unit: tag: Preferred_unit - value: '' - description: A local identifier or name that for the material sample used for - extracting nucleic acids, and subsequent sequencing. It can refer either to - the original material collected or to any derived sub-samples. It can have any - format, but we suggest that you make it concise, unique and consistent within - your lab, and as informative as possible. INSDC requires every sample name from - a single Submitter to be unique. Use of a globally unique identifier for the - field source_mat_id is recommended in addition to sample_name - title: sample name - examples: - - value: ISDsoil1 - in_subset: - - investigation - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - sample - slot_uri: MIXS:0001107 - multivalued: false - range: string - required: true - samp_pooling: - name: samp_pooling - description: Physical combination of several instances of like material, e.g. - RNA extracted from samples or dishes of cell cultures into one big aliquot of - cells. Please provide a short description of the samples that were pooled - title: sample pooling + value: gram, mole per liter, milligram per liter + description: Information about treatment involving use of herbicides; information + about treatment involving use of growth hormones; should include the name of + herbicide, amount administered, treatment regimen including how many times the + treatment was repeated, how long each treatment lasted, and the start and end + time of the entire treatment; can include multiple regimens + title: herbicide regimen examples: - - value: 5uL of extracted genomic DNA from 5 leaves were pooled + - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc keywords: - - pooling - - sample - slot_uri: MIXS:0001153 + - regimen + slot_uri: MIXS:0000561 multivalued: true range: string - samp_preserv: - name: samp_preserv - annotations: - Preferred_unit: - tag: Preferred_unit - value: milliliter - description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, - etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) - title: preservative added to sample + horizon_meth: + name: horizon_meth + description: Reference or method used in determining the horizon + title: horizon method from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sample - slot_uri: MIXS:0000463 + - horizon + - method + slot_uri: MIXS:0000321 multivalued: false range: string - required: false - recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ structured_pattern: - syntax: ^{name};{float} {unit}$ + syntax: ^{PMID}|{DOI}|{URL}$ interpolated: true partial_match: true - samp_purpose: - name: samp_purpose - annotations: - Expected_value: - tag: Expected_value - value: enumeration or {text} - description: The reason that the sample was collected - title: purpose of sampling - examples: - - value: field trial - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - purpose - string_serialization: '[active surveillance in response to an outbreak|active - surveillance not initiated by an outbreak|clinical trial|cluster investigation|environmental - assessment|farm sample|field trial|for cause|industry internal investigation|market - sample|passive surveillance|population based studies|research|research and development] - or {text}' - slot_uri: MIXS:0001151 - multivalued: false - samp_rep_biol: - name: samp_rep_biol - description: Measurements of biologically distinct samples that show biological - variation - title: biological sample replicate - examples: - - value: 6 replicates + host_age: + name: host_age + annotations: + Preferred_unit: + tag: Preferred_unit + value: year, day, hour + description: Age of host at the time of sampling; relevant scale depends on species + and study, e.g. Could be seconds for amoebae or centuries for trees + title: host age from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sample - slot_uri: MIXS:0001226 + - age + - host + - host. + slot_uri: MIXS:0000255 multivalued: false range: string - required: false - recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - samp_rep_tech: - name: samp_rep_tech - description: Repeated measurements of the same sample that show independent measures - of the noise associated with the equipment and the protocols - title: technical sample replicate - examples: - - value: 10 replicates + host_body_habitat: + name: host_body_habitat + description: Original body habitat where the sample was obtained from + title: host body habitat from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sample - slot_uri: MIXS:0001227 + - body + - habitat + - host + - host. + slot_uri: MIXS:0000866 multivalued: false range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - samp_room_id: - name: samp_room_id - description: Sampling room number. This ID should be consistent with the designations - on the building floor plans - title: sampling room ID or name - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - identifier - - room - slot_uri: MIXS:0000244 - multivalued: false - range: integer - required: false - recommended: false - samp_size: - name: samp_size - description: The total amount or size (volume (ml), mass (g) or area (m2) ) of - sample collected - title: amount or size of sample collected + host_body_mass_index: + name: host_body_mass_index + annotations: + Preferred_unit: + tag: Preferred_unit + value: kilogram per square meter + description: Body mass index, calculated as weight/(height)squared + title: host body-mass index examples: - - value: 5 liter - in_subset: - - nucleic acid sequence source + - value: 22 kilogram per square meter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sample - - size - slot_uri: MIXS:0000001 + - host + - host. + slot_uri: MIXS:0000317 multivalued: false range: string + required: false + recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - samp_sort_meth: - name: samp_sort_meth - description: Method by which samples are sorted; open face filter collecting total - suspended particles, prefilter to remove particles larger than X micrometers - in diameter, where common values of X would be 10 and 2.5 full size sorting - in a cascade impactor - title: sample size sorting method - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - method - - sample - - size - slot_uri: MIXS:0000216 - multivalued: true - range: string - required: false - recommended: false - samp_source_mat_cat: - name: samp_source_mat_cat + host_body_product: + name: host_body_product annotations: Expected_value: tag: Expected_value - value: GENEPIO:0001237 - description: This is the scientific role or category that the subject organism - or material has with respect to an investigation. This field accepts terms - listed under specimen source material category (http://purl.obolibrary.org/obo/GENEPIO_0001237 - or http://purl.obolibrary.org/obo/OBI_0100051) - title: sample source material category + value: FMA or UBERON + description: Substance produced by the body, e.g. Stool, mucus, where the sample + was obtained from. Use terms from the foundational model of anatomy ontology + (fma) or Uber-anatomy ontology (UBERON) + title: host body product examples: - - value: environmental (swab or sampling) [GENEPIO:0001732] + - value: mucus [FMA:66938] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - material - - sample - - source + - body + - host + - host. + - product string_serialization: '{termLabel} [{termID}]' - slot_uri: MIXS:0001154 + slot_uri: MIXS:0000888 multivalued: false - samp_stor_device: - name: samp_stor_device + required: false + recommended: false + host_body_site: + name: host_body_site annotations: Expected_value: tag: Expected_value - value: NCIT:C4318 - description: The container used to store the sample. This field accepts terms - listed under container (http://purl.obolibrary.org/obo/NCIT_C43186). If the - proper descriptor is not listed please use text to describe the storage device - title: sample storage device - examples: - - value: Whirl Pak sampling bag [GENEPIO:0002122] + value: FMA or UBERON + description: Name of body site where the sample was obtained from, such as a specific + organ or tissue (tongue, lung etc...). Use terms from the foundational model + of anatomy ontology (fma) or the Uber-anatomy ontology (UBERON) + title: host body site from_schema: https://w3id.org/mixs-6-2-rc keywords: - - device - - sample - - storage - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001228 + - body + - host + - host. + - site + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0000867 multivalued: false - samp_stor_media: - name: samp_stor_media - description: The liquid that is added to the sample collection device prior to - sampling. If the sample is pre-hydrated, indicate the liquid media the sample - is pre-hydrated with for storage purposes. This field accepts terms listed under - microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067). - If the proper descriptor is not listed please use text to describe the sample - storage media - title: sample storage media - examples: - - value: peptone water medium [MICRO:0000548] + required: false + recommended: false + host_body_temp: + name: host_body_temp + annotations: + Preferred_unit: + tag: Preferred_unit + value: degree Celsius + description: Core body temperature of the host when sample was collected + title: host body temperature from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sample - - storage - slot_uri: MIXS:0001229 + - body + - host + - host. + - temperature + slot_uri: MIXS:0000274 multivalued: false range: string - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$ + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{text}|({termLabel} \[{termID}\])$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - samp_store_dur: - name: samp_store_dur - description: Duration for which the sample was stored. Indicate the duration for - which the sample was stored written in ISO 8601 format - title: sample storage duration + host_cellular_loc: + name: host_cellular_loc + description: 'The localization of the symbiotic host organism within the host + from which it was sampled: e.g. intracellular if the symbiotic host organism + is localized within the cells or extracellular if the symbiotic host organism + is localized outside of cells' + title: host cellular location examples: - - value: P1Y6M + - value: extracellular from_schema: https://w3id.org/mixs-6-2-rc keywords: - - duration - - period - - sample - - storage - slot_uri: MIXS:0000116 + - host + - host. + - location + slot_uri: MIXS:0001313 + range: HOST_CELLULAR_LOC_ENUM + recommended: true + host_color: + name: host_color + description: The color of host + title: host color + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - host + - host. + slot_uri: MIXS:0000260 multivalued: false range: string - pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ - structured_pattern: - syntax: ^{duration}$ - interpolated: true - partial_match: true - samp_store_loc: - name: samp_store_loc - annotations: - Expected_value: - tag: Expected_value - value: location name - description: Location at which sample was stored, usually name of a specific freezer/room - title: sample storage location + required: false + recommended: false + host_common_name: + name: host_common_name + annotations: + Preferred_unit: + tag: Preferred_unit + value: '' + description: Common name of the host + title: host common name + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - host + - host. + slot_uri: MIXS:0000248 + multivalued: false + range: string + host_dependence: + name: host_dependence + description: Type of host dependence for the symbiotic host organism to its host + title: host dependence examples: - - value: Freezer no:5 + - value: obligate from_schema: https://w3id.org/mixs-6-2-rc keywords: - - location - - sample - - storage - string_serialization: '{text}' - slot_uri: MIXS:0000755 + - host + - host. + slot_uri: MIXS:0001315 multivalued: false - samp_store_sol: - name: samp_store_sol + range: HOST_DEPENDENCE_ENUM + required: true + host_diet: + name: host_diet + description: Type of diet depending on the host, for animals omnivore, herbivore + etc., for humans high-fat, meditteranean etc.; can include multiple diet types + title: host diet + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - diet + - host + - host. + slot_uri: MIXS:0000869 + multivalued: true + range: string + required: false + recommended: false + host_disease_stat: + name: host_disease_stat annotations: Expected_value: tag: Expected_value - value: solution name - description: Solution within which sample was stored, if any - title: sample storage solution - examples: - - value: 5% ethanol + value: disease name or Disease Ontology term + description: List of diseases with which the host has been diagnosed; can include + multiple diagnoses. The value of the field depends on host; for humans the terms + should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, + non-human host diseases are free text + title: host disease status + in_subset: + - nucleic acid sequence source from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sample - - storage - string_serialization: '{text}' - slot_uri: MIXS:0001317 + - disease + - host + - host. + - status + string_serialization: '{termLabel} [{termID}]|{text}' + slot_uri: MIXS:0000031 multivalued: false - required: false - recommended: false - samp_store_temp: - name: samp_store_temp + host_dry_mass: + name: host_dry_mass annotations: Preferred_unit: tag: Preferred_unit - value: degree Celsius - description: Temperature at which sample was stored, e.g. -80 degree Celsius - title: sample storage temperature + value: kilogram, gram + description: Measurement of dry mass + title: host dry mass examples: - - value: -80 degree Celsius + - value: 500 gram from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sample - - storage - - temperature - slot_uri: MIXS:0000110 + - dry + - host + - host. + - mass + slot_uri: MIXS:0000257 multivalued: false range: string required: false @@ -13690,816 +11601,797 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - samp_subtype: - name: samp_subtype - description: Name of sample sub-type. For example if "sample type" is "Produced - Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, - please propose entry in "additional info" field - title: sample subtype - examples: - - value: biofilm - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - sample - slot_uri: MIXS:0000999 - multivalued: false - range: SAMP_SUBTYPE_ENUM - recommended: true - samp_surf_moisture: - name: samp_surf_moisture - description: Degree of water held on a sampled surface. If present, user can - state the degree of water held on surface (intermittent moisture, submerged). - If no surface moisture is present indicate not present - title: sample surface moisture - examples: - - value: submerged + host_fam_rel: + name: host_fam_rel + annotations: + Expected_value: + tag: Expected_value + value: relationship type;arbitrary identifier + description: Relationships to other hosts in the same study; can include multiple + relationships + title: host family relationship from_schema: https://w3id.org/mixs-6-2-rc keywords: - - moisture - - sample - - surface - slot_uri: MIXS:0001256 + - family + - host + - host. + - relationship + string_serialization: '{text};{text}' + slot_uri: MIXS:0000872 multivalued: true - range: SAMP_SURF_MOISTURE_ENUM required: false recommended: false - samp_taxon_id: - name: samp_taxon_id - description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa - sample. Use 'synthetic metagenome for mock community/positive controls, or - 'blank sample' for negative controls - title: taxonomy ID of DNA sample + host_genotype: + name: host_genotype + description: Observed genotype + title: host genotype + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - host + - host. + slot_uri: MIXS:0000365 + multivalued: false + range: string + host_growth_cond: + name: host_growth_cond + description: Literature reference giving growth conditions of the host + title: host growth conditions examples: - - value: Gut Metagenome [NCBITaxon:749906] - in_subset: - - investigation + - value: https://academic.oup.com/icesjms/article/68/2/349/617247 from_schema: https://w3id.org/mixs-6-2-rc keywords: - - dna - - identifier - - sample - - taxon - slot_uri: MIXS:0001320 + - condition + - growth + - host + - host. + slot_uri: MIXS:0000871 multivalued: false range: string - required: true - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$ + required: false + recommended: false + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{text} \[{NCBItaxon_id}\]$ + syntax: ^{PMID}|{DOI}|{URL}|{text}$ interpolated: true partial_match: true - samp_time_out: - name: samp_time_out + host_height: + name: host_height annotations: - Expected_value: - tag: Expected_value - value: time Preferred_unit: tag: Preferred_unit - value: hour - description: The recent and long term history of outside sampling - title: sampling time outside + value: centimeter, millimeter, meter + description: The height of subject + title: host height from_schema: https://w3id.org/mixs-6-2-rc keywords: - - time - string_serialization: '{float}' - slot_uri: MIXS:0000196 + - height + - host + - host. + slot_uri: MIXS:0000264 multivalued: false - required: false - recommended: false - samp_transport_cond: - name: samp_transport_cond + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + host_hiv_stat: + name: host_hiv_stat annotations: Expected_value: tag: Expected_value - value: measurement value;measurement value - Preferred_unit: - tag: Preferred_unit - value: days;degree Celsius - description: Sample transport duration (in days or hrs) and temperature the sample - was exposed to (e.g. 5.5 days; 20 C) - title: sample transport conditions + value: HIV status;HAART initiation status + description: HIV status of subject, if yes HAART initiation status should also + be indicated as [YES or NO] + title: host HIV status examples: - - value: 5 days;-20 degree Celsius + - value: yes;yes from_schema: https://w3id.org/mixs-6-2-rc keywords: - - condition - - sample - - transport - string_serialization: '{float} {unit};{float} {unit}' - slot_uri: MIXS:0000410 + - host + - host. + - status + string_serialization: '{boolean};{boolean}' + slot_uri: MIXS:0000265 multivalued: false required: false recommended: false - samp_transport_cont: - name: samp_transport_cont - description: Conatiner in which the sample was stored during transport. Indicate - the location name - title: sample transport container - examples: - - value: cooler + host_infra_spec_name: + name: host_infra_spec_name + description: Taxonomic information about the host below subspecies level + title: host infra-specific name from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sample - - transport - slot_uri: MIXS:0001230 + - host + - host. + slot_uri: MIXS:0000253 multivalued: false - range: SAMP_TRANSPORT_CONT_ENUM + range: string required: false recommended: false - samp_transport_dur: - name: samp_transport_dur - annotations: - Preferred_unit: - tag: Preferred_unit - value: days - description: The duration of time from when the sample was collected until processed. - Indicate the duration for which the sample was stored written in ISO 8601 format - title: sample transport duration - examples: - - value: P10D + host_infra_spec_rank: + name: host_infra_spec_rank + description: Taxonomic rank information about the host below subspecies level, + such as variety, form, rank etc + title: host infra-specific rank from_schema: https://w3id.org/mixs-6-2-rc keywords: - - duration - - period - - sample - - transport - slot_uri: MIXS:0001231 + - host + - host. + - rank + slot_uri: MIXS:0000254 multivalued: false range: string required: false recommended: false - pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ - structured_pattern: - syntax: ^{duration}$ - interpolated: true - partial_match: true - samp_transport_temp: - name: samp_transport_temp + host_last_meal: + name: host_last_meal annotations: Expected_value: tag: Expected_value - value: text or measurement value - Preferred_unit: - tag: Preferred_unit - value: degree Celsius - description: Temperature at which sample was transported, e.g. -20 or 4 degree - Celsius - title: sample transport temperature - examples: - - value: 4 degree Celsius + value: content;duration + description: Content of last meal and time since feeding; can include multiple + values + title: host last meal from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sample - - temperature - - transport - string_serialization: '{float} {unit} {text}' - slot_uri: MIXS:0001232 - multivalued: false + - host + - host. + string_serialization: '{text};{duration}' + slot_uri: MIXS:0000870 + multivalued: true required: false recommended: false - samp_tvdss: - name: samp_tvdss + host_length: + name: host_length annotations: - Expected_value: - tag: Expected_value - value: measurement value or measurement value range Preferred_unit: tag: Preferred_unit - value: meter - description: Depth of the sample i.e. The vertical distance between the sea level - and the sampled position in the subsurface. Depth can be reported as an interval - for subsurface samples e.g. 1325.75-1362.25 m - title: sample true vertical depth subsea - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - depth - - sample - string_serialization: '{float}-{float} {unit}' - slot_uri: MIXS:0000409 - multivalued: false - recommended: true - samp_type: - name: samp_type - description: The type of material from which the sample was obtained. For the - Hydrocarbon package, samples include types like core, rock trimmings, drill - cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, - produced water, injected water, swabs, etc. For the Food Package, samples are - usually categorized as food, body products or tissues, or environmental material. - This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246) - title: sample type + value: centimeter, millimeter, meter + description: The length of subject + title: host length examples: - - value: built environment sample [GENEPIO:0001248] + - value: 1 meter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sample - - type - slot_uri: MIXS:0000998 + - host + - host. + - length + slot_uri: MIXS:0000256 multivalued: false range: string - required: true - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext + host_life_stage: + name: host_life_stage annotations: - Preferred_unit: - tag: Preferred_unit - value: milliliter, gram, milligram, square centimeter - description: 'Volume (ml) or mass (g) of total collected sample processed for - DNA extraction. Note: total sample collected should be entered under the term - Sample Size (MIXS:0000001)' - title: sample volume or weight for DNA extraction - examples: - - value: 1500 milliliter - in_subset: - - nucleic acid sequence source + Expected_value: + tag: Expected_value + value: stage + description: Description of life stage of host + title: host life stage from_schema: https://w3id.org/mixs-6-2-rc keywords: - - dna - - sample - - volume - - weight - slot_uri: MIXS:0000111 + - host + - host. + - life + string_serialization: '{text}' + slot_uri: MIXS:0000251 multivalued: false - range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - samp_weather: - name: samp_weather - description: The weather on the sampling day - title: sampling day weather + host_number: + name: host_number + annotations: + Expected_value: + tag: Expected_value + value: count + description: Number of symbiotic host individuals pooled at the time of collection + title: host number individual examples: - - value: foggy + - value: '3' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - day - - weather - slot_uri: MIXS:0000827 + - host + - host. + - number + string_serialization: '{float} m' + slot_uri: MIXS:0001305 multivalued: false - range: SAMP_WEATHER_ENUM required: false recommended: false - samp_well_name: - name: samp_well_name - description: Name of the well (e.g. BXA1123) where sample was taken - title: sample well name + host_occupation: + name: host_occupation + description: Most frequent job performed by subject + title: host occupation + comments: + - Couldn't convert host_occupation with value veterinary to integer + - almost all host_occupation values in the NCBI biosample_set are strings, not + integers + examples: + - value: veterinary from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sample - slot_uri: MIXS:0000296 - multivalued: false + - host + - host. + slot_uri: MIXS:0000896 range: string - recommended: true - saturates_pc: - name: saturates_pc + required: false + recommended: false + host_of_host_coinf: + name: host_of_host_coinf annotations: - Preferred_unit: - tag: Preferred_unit - value: percent - description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis - method that divides crude oil components according to their polarizability - and polarity. There are three main methods to obtain SARA results. The most - popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: - https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' - title: saturates wt% - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000131 - multivalued: false - range: string - recommended: true - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{name};{float} {unit}$ - interpolated: true - partial_match: true - sc_lysis_approach: - name: sc_lysis_approach - description: Method used to free DNA from interior of the cell(s) or particle(s) - title: single cell or viral particle lysis approach + Expected_value: + tag: Expected_value + value: species name of coinfecting organism(s) + description: The taxonomic name of any coinfecting organism observed in a symbiotic + relationship with the host of the sampled host organism. e.g. where a sample + collected from a host trematode species (A) which was collected from a host_of_host + fish (B) that was also infected with a nematode (C), the value here would be + (C) the nematode {species name} or {common name}. Multiple co-infecting species + may be added in a comma-separated list. For listing symbiotic organisms associated + with the host (A) use the term Observed host symbiont + title: observed coinfecting organisms in host of host examples: - - value: enzymatic - in_subset: - - sequencing + - value: Maritrema novaezealandense from_schema: https://w3id.org/mixs-6-2-rc keywords: - - particle - - single - slot_uri: MIXS:0000076 + - host + - host. + - observed + - organism + string_serialization: '{text}' + slot_uri: MIXS:0001310 multivalued: false - range: SC_LYSIS_APPROACH_ENUM - sc_lysis_method: - name: sc_lysis_method + required: false + recommended: false + host_of_host_disease: + name: host_of_host_disease annotations: Expected_value: tag: Expected_value - value: kit, protocol name - description: Name of the kit or standard protocol used for cell(s) or particle(s) - lysis - title: single cell or viral particle lysis kit protocol - examples: - - value: ambion single cell lysis kit - in_subset: - - sequencing + value: disease name or Disease Ontology term + description: List of diseases with which the host of the symbiotic host organism + has been diagnosed; can include multiple diagnoses. The value of the field depends + on host; for humans the terms should be chosen from the DO (Human Disease Ontology) + at https://www.disease-ontology.org, non-human host diseases are free text + title: host of the symbiotic host disease status + examples: + - value: rabies [DOID:11260] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - kit - - particle - - protocol - - single - string_serialization: '{text}' - slot_uri: MIXS:0000054 - multivalued: false - season: - name: season + - disease + - host + - host. + - status + - symbiosis + string_serialization: '{termLabel} [{termID}]|{text}' + slot_uri: MIXS:0001319 + multivalued: true + required: false + recommended: false + host_of_host_env_loc: + name: host_of_host_env_loc annotations: Expected_value: tag: Expected_value - value: autumn [NCIT:C94733], spring [NCIT:C94731], summer [NCIT:C94732], winter - [NCIT:C94730] - description: The season when sampling occurred. Any of the four periods into which - the year is divided by the equinoxes and solstices. This field accepts terms - listed under season (http://purl.obolibrary.org/obo/NCIT_C94729) - title: season - comments: - - autumn [NCIT:C94733] does not match ^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$ - - would require ^\\S+.*\\S+ \\[[a-zA-Z]{2,}:[a-zA-Z0-9]\\]$ + value: UBERON term(s), multiple values can be separated by pipes + description: For a symbiotic host organism the local anatomical environment within + its host may have causal influences. Report the anatomical entity(s) which are + in the direct environment of the symbiotic host organism being sampled and which + you believe have significant causal influences on your sample or specimen. For + example, if the symbiotic host organism being sampled is an intestinal worm, + its local environmental context will be the term for intestine from UBERON (http://uberon.github.io/) + title: host of the symbiotic host local environmental context examples: - - value: autumn [NCIT:C94733] + - value: small intestine[uberon:0002108] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - season - string_serialization: '{termLabel} [{termID}]' - slot_uri: MIXS:0000829 - range: string + - context + - environmental + - host + - host. + - symbiosis + string_serialization: small intestine [UBERON:0002108] + slot_uri: MIXS:0001325 + multivalued: true required: false recommended: false - pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:[a-zA-Z0-9]+\]$ - season_environment: - name: season_environment - description: Treatment involving an exposure to a particular season (e.g. Winter, - summer, rabi, rainy etc.), treatment regimen including how many times the treatment - was repeated, how long each treatment lasted, and the start and end time of - the entire treatment - title: seasonal environment + host_of_host_env_med: + name: host_of_host_env_med + annotations: + Expected_value: + tag: Expected_value + value: An ontology term for a material such as a tissue type or excreted substance + description: 'Report the environmental material(s) immediately surrounding the + symbiotic host organism at the time of sampling. This usually will be a tissue + or substance type from the host, but may be another material if the symbiont + is external to the host. We recommend using classes from the UBERON ontology, + but subclasses of ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483) + may also be used. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS + . Terms from other OBO ontologies are permissible as long as they reference + mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities + (e.g. intestines, heart).MIxS . Terms from other OBO ontologies are permissible + as long as they reference mass/volume nouns (e.g. air, water, blood) and not + discrete, countable entities (e.g. intestines, heart)' + title: host of the symbiotic host environemental medium examples: - - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: feces[uberon:0001988] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - environment - - season - slot_uri: MIXS:0001068 - multivalued: true - range: string - season_humidity: - name: season_humidity - description: Average humidity of the region throughout the growing season - title: mean seasonal humidity - comments: - - percent or float? - examples: - - value: '0.25' + - environmental + - host + - host. + - symbiosis + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0001326 + required: false + recommended: false + host_of_host_fam_rel: + name: host_of_host_fam_rel + annotations: + Expected_value: + tag: Expected_value + value: relationship type;arbitrary identifier + description: Familial relationship of the host of the symbiotic host organisms + to other hosts of symbiotic host organism in the same study; can include multiple + relationships + title: host of the symbiotic host family relationship from_schema: https://w3id.org/mixs-6-2-rc keywords: - - humidity - - mean - - season - slot_uri: MIXS:0001148 - range: float + - family + - host + - host. + - relationship + - symbiosis + string_serialization: '{text};{text}' + slot_uri: MIXS:0001328 + multivalued: true required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - season_precpt: - name: season_precpt - annotations: - Preferred_unit: - tag: Preferred_unit - value: millimeter - description: The average of all seasonal precipitation values known, or an estimated - equivalent value derived by such methods as regional indexes or Isohyetal maps - title: mean seasonal precipitation - examples: - - value: 75 millimeters + host_of_host_geno: + name: host_of_host_geno + description: Observed genotype of the host of the symbiotic host organism + title: host of the symbiotic host genotype from_schema: https://w3id.org/mixs-6-2-rc keywords: - - mean - - season - slot_uri: MIXS:0000645 + - host + - host. + - symbiosis + slot_uri: MIXS:0001331 multivalued: false range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - season_temp: - name: season_temp + host_of_host_gravid: + name: host_of_host_gravid annotations: - Preferred_unit: - tag: Preferred_unit - value: degree Celsius - description: Mean seasonal temperature - title: mean seasonal temperature - examples: - - value: 18 degree Celsius + Expected_value: + tag: Expected_value + value: gravidity status;timestamp + description: Whether or not the host of the symbiotic host organism is gravid, + and if yes date due or date post-conception, specifying which is used + title: host of the symbiotic host gravidity from_schema: https://w3id.org/mixs-6-2-rc keywords: - - mean - - season - - temperature - slot_uri: MIXS:0000643 + - host + - host. + - symbiosis + string_serialization: '{boolean};{timestamp}' + slot_uri: MIXS:0001333 multivalued: false - range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - season_use: - name: season_use - description: The seasons the space is occupied - title: seasonal use - examples: - - value: Winter + host_of_host_infname: + name: host_of_host_infname + description: Taxonomic name information of the host of the symbiotic host organism + below subspecies level + title: host of the symbiotic host infra-specific name from_schema: https://w3id.org/mixs-6-2-rc keywords: - - season - - use - slot_uri: MIXS:0000830 + - host + - host. + - symbiosis + slot_uri: MIXS:0001329 multivalued: false - range: SEASON_USE_ENUM + range: string required: false recommended: false - secondary_treatment: - name: secondary_treatment - annotations: - Expected_value: - tag: Expected_value - value: secondary treatment type - description: The process for substantially degrading the biological content of - the sewage - title: secondary treatment + host_of_host_infrank: + name: host_of_host_infrank + description: Taxonomic rank information about the host of the symbiotic host organism + below subspecies level, such as variety, form, rank etc + title: host of the symbiotic host infra-specific rank from_schema: https://w3id.org/mixs-6-2-rc keywords: - - secondary - - treatment - string_serialization: '{text}' - slot_uri: MIXS:0000351 + - host + - host. + - rank + - symbiosis + slot_uri: MIXS:0001330 multivalued: false + range: string required: false recommended: false - sediment_type: - name: sediment_type - description: Information about the sediment type based on major constituents - title: sediment type + host_of_host_name: + name: host_of_host_name + description: Common name of the host of the symbiotic host organism + title: host of the symbiotic host common name examples: - - value: biogenous + - value: snail from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sediment - - type - slot_uri: MIXS:0001078 - multivalued: false - range: SEDIMENT_TYPE_ENUM + - host + - host. + - symbiosis + slot_uri: MIXS:0001324 + range: string required: false recommended: false - seq_meth: - name: seq_meth - description: Sequencing machine used. Where possible the term should be taken - from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103) - title: sequencing method - examples: - - value: 454 Genome Sequencer FLX [OBI:0000702] - in_subset: - - sequencing - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - method - slot_uri: MIXS:0000050 - multivalued: false - range: string - required: true - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$ - structured_pattern: - syntax: ^{text}|({termLabel} \[{termID}\])$ - interpolated: true - partial_match: true - seq_quality_check: - name: seq_quality_check + host_of_host_pheno: + name: host_of_host_pheno annotations: Expected_value: tag: Expected_value - value: none or manually edited - description: Indicate if the sequence has been called by automatic systems (none) - or undergone a manual editing procedure (e.g. by inspecting the raw data or - chromatograms). Applied only for sequences that are not submitted to SRA,ENA - or DRA - title: sequence quality check - examples: - - value: none - in_subset: - - sequencing + value: phenotype of the host of the symbiotic organism; PATO + description: Phenotype of the host of the symbiotic host organism. For phenotypic + quality ontology (PATO) terms, see http://purl.bioontology.org/ontology/pato + title: host of the symbiotic host phenotype from_schema: https://w3id.org/mixs-6-2-rc keywords: - - quality - slot_uri: MIXS:0000051 + - host + - host. + - symbiosis + string_serialization: '{term}' + slot_uri: MIXS:0001332 multivalued: false - range: SEQ_QUALITY_CHECK_ENUM - sequencing_kit: - name: sequencing_kit - annotations: - Expected_value: - tag: Expected_value - value: name of sequencing kit used - description: Pre-filled, ready-to-use reagent cartridges. Used to produce improved - chemistry, cluster density and read length as well as improve quality (Q) scores. - Reagent components are encoded to interact with the sequencing system to validate - compatibility with user-defined applications. Indicate name of the sequencing - kit - title: sequencing kit + required: false + recommended: false + host_of_host_sub_id: + name: host_of_host_sub_id + description: 'A unique identifier by which each host of the symbiotic host organism + subject can be referred to, de-identified, e.g. #H14' + title: host of the symbiotic host subject id examples: - - value: NextSeq 500/550 High Output Kit v2.5 (75 Cycles) + - value: H3 from_schema: https://w3id.org/mixs-6-2-rc keywords: - - kit - string_serialization: '{text}' - slot_uri: MIXS:0001155 + - host + - host. + - identifier + - symbiosis + slot_uri: MIXS:0001327 multivalued: false + range: string required: false recommended: false - sequencing_location: - name: sequencing_location - description: The location the sequencing run was performed. Indicate the name - of the lab or core facility where samples were sequenced - title: sequencing location + host_of_host_taxid: + name: host_of_host_taxid + annotations: + Expected_value: + tag: Expected_value + value: NCBI taxon identifier of the host of the symbiotic taxon organism + description: NCBI taxon id of the host of the symbiotic host organism + title: host of the symbiotic host taxon id examples: - - value: University of Maryland Genomics Resource Center + - value: '145637' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - location - slot_uri: MIXS:0001156 + - host + - host. + - identifier + - symbiosis + - taxon + string_serialization: '{integer}' + slot_uri: MIXS:0001306 multivalued: false - range: string required: false recommended: false - serovar_or_serotype: - name: serovar_or_serotype - description: A characterization of a cell or microorganism based on the antigenic - properties of the molecules on its surface. Indicate the name of a serovar or - serotype of interest. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). - This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy - title: serovar or serotype - examples: - - value: Escherichia coli strain O157:H7 [NCIT:C86883] + host_of_host_totmass: + name: host_of_host_totmass + description: Total mass of the host of the symbiotic host organism at collection, + the unit depends on the host + title: host of the symbiotic host total mass from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0001157 - multivalued: true + keywords: + - host + - host. + - mass + - symbiosis + - total + slot_uri: MIXS:0001334 + multivalued: false range: string required: false recommended: false - pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^({termLabel} \[{termID}\])|{integer}$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - sewage_type: - name: sewage_type + host_phenotype: + name: host_phenotype annotations: Expected_value: tag: Expected_value - value: sewage type name - description: Type of wastewater treatment plant as municipial or industrial - title: sewage type + value: PATO or HP + description: Phenotype of human or other host. Use terms from the phenotypic quality + ontology (pato) or the Human Phenotype Ontology (HP) + title: host phenotype from_schema: https://w3id.org/mixs-6-2-rc keywords: - - type - string_serialization: '{text}' - slot_uri: MIXS:0000215 - multivalued: false - required: false - recommended: false - sexual_act: - name: sexual_act - annotations: - Expected_value: - tag: Expected_value - value: partner sex;frequency - description: Current sexual partner and frequency of sex - title: sexual activity - from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text}' - slot_uri: MIXS:0000285 + - host + - host. + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0000874 multivalued: false - required: false - recommended: false - shad_dev_water_mold: - name: shad_dev_water_mold - description: Signs of the presence of mold or mildew on the shading device - title: shading device signs of water/mold + host_pred_appr: + name: host_pred_appr + description: Tool or approach used for host prediction + title: host prediction approach examples: - - value: no presence of mold visible + - value: CRISPR spacer match + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - device - slot_uri: MIXS:0000834 + - host + - host. + - predict + slot_uri: MIXS:0000088 multivalued: false - range: SHARED_ENUM_1 - required: false - recommended: false - shading_device_cond: - name: shading_device_cond - description: The physical condition of the shading device at the time of sampling - title: shading device condition + range: HOST_PRED_APPR_ENUM + host_pred_est_acc: + name: host_pred_est_acc + description: For each tool or approach used for host prediction, estimated false + discovery rates should be included, either computed de novo or from the literature + title: host prediction estimated accuracy examples: - - value: new + - value: 'CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host + genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048)' + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - condition - - device - slot_uri: MIXS:0000831 + - host + - host. + - predict + slot_uri: MIXS:0000089 multivalued: false - range: SHARED_ENUM_2 - required: false - recommended: false - shading_device_loc: - name: shading_device_loc - description: The location of the shading device in relation to the built structure - title: shading device location + range: string + host_pulse: + name: host_pulse + annotations: + Preferred_unit: + tag: Preferred_unit + value: beats per minute + description: Resting pulse, measured as beats per minute + title: host pulse examples: - - value: exterior + - value: 65 beats per minute from_schema: https://w3id.org/mixs-6-2-rc keywords: - - device - - location - slot_uri: MIXS:0000832 + - host + - host. + slot_uri: MIXS:0000333 multivalued: false - range: SHADING_DEVICE_LOC_ENUM + range: string required: false recommended: false - shading_device_mat: - name: shading_device_mat + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + host_sex: + name: host_sex annotations: Expected_value: tag: Expected_value - value: material name - description: The material the shading device is composed of - title: shading device material + value: enumeration + description: Gender or physical sex of the host + title: host sex + comments: + - example of non-binary from Excel sheets does not match any of the enumerated + values from_schema: https://w3id.org/mixs-6-2-rc keywords: - - device - - material - string_serialization: '{text}' - slot_uri: MIXS:0000245 - multivalued: false + - host + - host. + string_serialization: '[female|hermaphrodite|non-binary|male|transgender|transgender + (female to male)|transgender (male to female) + + |undeclared]' + slot_uri: MIXS:0000811 required: false recommended: false - shading_device_type: - name: shading_device_type - description: The type of shading device - title: shading device type + host_shape: + name: host_shape + description: Morphological shape of host + title: host shape examples: - - value: slatted aluminum - description: was slatted aluminum awning + - value: round from_schema: https://w3id.org/mixs-6-2-rc keywords: - - device - - type - slot_uri: MIXS:0000835 - range: SHADING_DEVICE_TYPE_ENUM + - host + - host. + slot_uri: MIXS:0000261 + multivalued: false + range: string required: false recommended: false - sieving: - name: sieving + host_spec_range: + name: host_spec_range annotations: Expected_value: tag: Expected_value - value: design name and/or size;amount - description: Collection design of pooled samples and/or sieve size and amount - of sample sieved - title: sieving + value: NCBI taxid + description: The range and diversity of host species that an organism is capable + of infecting, defined by NCBI taxonomy identifier + title: host specificity or range + examples: + - value: '9606' + in_subset: + - nucleic acid sequence source from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000322 - multivalued: false - silicate: - name: silicate - annotations: - Preferred_unit: - tag: Preferred_unit - value: micromole per liter - description: Concentration of silicate - title: silicate + keywords: + - host + - host. + - range + string_serialization: '{integer}' + slot_uri: MIXS:0000030 + multivalued: true + host_specificity: + name: host_specificity + description: 'Level of specificity of symbiont-host interaction: e.g. generalist + (symbiont able to establish associations with distantly related hosts) or species-specific' + title: host specificity examples: - - value: 0.05 micromole per liter + - value: species-specific from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000184 + keywords: + - host + - host. + slot_uri: MIXS:0001308 + multivalued: false + range: HOST_SPECIFICITY_ENUM + recommended: true + host_subject_id: + name: host_subject_id + description: A unique identifier by which each subject can be referred to, de-identified + title: host subject id + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - host + - host. + - identifier + slot_uri: MIXS:0000861 multivalued: false range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - sim_search_meth: - name: sim_search_meth - description: Tool used to compare ORFs with database, along with version and cutoffs - used - title: similarity search method + host_subspecf_genlin: + name: host_subspecf_genlin + annotations: + Expected_value: + tag: Expected_value + value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, + e.g. serovar, biotype, ecotype, variety, cultivar + description: Information about the genetic distinctness of the host organism below + the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, + or any relevant genetic typing schemes like Group I plasmid. Subspecies should + not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage + name and the lineage rank separated by a colon, e.g., biovar:abc123 + title: host subspecific genetic lineage examples: - - value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score - in_subset: - - sequencing + - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - method - slot_uri: MIXS:0000063 + - host + - host. + - lineage + string_serialization: '{rank name}:{text}' + slot_uri: MIXS:0001318 + multivalued: true + required: false + recommended: false + host_substrate: + name: host_substrate + description: The growth substrate of the host + title: host substrate + examples: + - value: rock + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - host + - host. + slot_uri: MIXS:0000252 multivalued: false range: string - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{software};{version};{parameters}$ - interpolated: true - partial_match: true - size_frac: - name: size_frac + required: false + recommended: false + host_symbiont: + name: host_symbiont annotations: Expected_value: tag: Expected_value - value: filter size value range - description: Filtering pore size used in sample preparation - title: size fraction selected - examples: - - value: 0-0.22 micrometer - in_subset: - - nucleic acid sequence source + value: species name or common name + description: The taxonomic name of the organism(s) found living in mutualistic, + commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont + can have its own symbionts. For example, parasites may have hyperparasites (=parasites + of the parasite) + title: observed host symbionts from_schema: https://w3id.org/mixs-6-2-rc keywords: - - fraction - - size - string_serialization: '{float}-{float} {unit}' - slot_uri: MIXS:0000017 + - host + - host. + - observed + - symbiosis + string_serialization: '{text}' + slot_uri: MIXS:0001298 + multivalued: true + required: false + recommended: false + host_taxid: + name: host_taxid + annotations: + Expected_value: + tag: Expected_value + value: NCBI taxon identifier + description: NCBI taxon id of the host, e.g. 9606 + title: host taxid + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - host + - host. + - taxon + slot_uri: MIXS:0000250 multivalued: false - size_frac_low: - name: size_frac_low + host_tot_mass: + name: host_tot_mass annotations: Preferred_unit: tag: Preferred_unit - value: micrometer - description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. - Materials larger than the size threshold are excluded from the sample - title: size-fraction lower threshold - examples: - - value: 0.2 micrometer + value: kilogram, gram + description: Total mass of the host at collection, the unit depends on host + title: host total mass from_schema: https://w3id.org/mixs-6-2-rc keywords: - - lower - slot_uri: MIXS:0000735 + - host + - host. + - mass + - total + slot_uri: MIXS:0000263 multivalued: false range: string - required: false - recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - size_frac_up: - name: size_frac_up + host_wet_mass: + name: host_wet_mass annotations: Preferred_unit: tag: Preferred_unit - value: micrometer - description: Mesh or pore size of the device used to retain the sample. Materials - smaller than the size threshold are excluded from the sample - title: size-fraction upper threshold + value: kilogram, gram + description: Measurement of wet mass + title: host wet mass examples: - - value: 20 micrometer + - value: 1500 gram from_schema: https://w3id.org/mixs-6-2-rc keywords: - - upper - slot_uri: MIXS:0000736 + - host + - host. + - mass + - wet + slot_uri: MIXS:0000567 multivalued: false range: string required: false @@ -14510,43 +12402,27 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - slope_aspect: - name: slope_aspect - annotations: - Preferred_unit: - tag: Preferred_unit - value: degree - description: The direction a slope faces. While looking down a slope use a compass - to record the direction you are facing (direction or degrees); e.g., nw or 315 - degrees. This measure provides an indication of sun and wind exposure that will - influence soil temperature and evapotranspiration - title: slope aspect - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - slope - slot_uri: MIXS:0000647 - multivalued: false - range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - slope_gradient: - name: slope_gradient - annotations: - Preferred_unit: - tag: Preferred_unit - value: percentage - description: Commonly called 'slope'. The angle between ground surface and a horizontal - line (in percent). This is the direction that overland water would flow. This - measure is usually taken with a hand level meter or clinometer - title: slope gradient + hrt: + name: hrt + description: Whether subject had hormone replacement theraphy, and if yes start + date + title: HRT + examples: + - value: '2013-03-25T12:42:31+01:00' + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000969 + multivalued: false + range: datetime + required: false + recommended: false + humidity: + name: humidity + description: Amount of water vapour in the air, at the time of sampling + title: humidity from_schema: https://w3id.org/mixs-6-2-rc keywords: - - slope - slot_uri: MIXS:0000646 + - humidity + slot_uri: MIXS:0000100 multivalued: false range: string pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? @@ -14555,52 +12431,122 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - sludge_retent_time: - name: sludge_retent_time + humidity_regm: + name: humidity_regm annotations: + Expected_value: + tag: Expected_value + value: humidity value;treatment interval and duration Preferred_unit: tag: Preferred_unit - value: hours - description: The time activated sludge remains in reactor - title: sludge retention time + value: gram per cubic meter + description: Information about treatment involving an exposure to varying degree + of humidity; information about treatment involving use of growth hormones; should + include amount of humidity administered, treatment regimen including how many + times the treatment was repeated, how long each treatment lasted, and the start + and end time of the entire treatment; can include multiple regimens + title: humidity regimen + examples: + - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc keywords: - - time - slot_uri: MIXS:0000669 + - humidity + - regimen + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000568 + multivalued: true + required: false + recommended: false + hygienic_area: + name: hygienic_area + annotations: + Expected_value: + tag: Expected_value + value: Expected value + description: The subdivision of areas within a food production facility according + to hygienic requirements. This field accepts terms listed under hygienic food + production area (http://purl.obolibrary.org/obo/ENVO). Please add a term that + most accurately indicates the hygienic area your sample was taken from according + to the definitions provided + title: hygienic food production area + examples: + - value: Low Hygiene Area + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - area + - food + - production + string_serialization: '{text}' + slot_uri: MIXS:0001253 multivalued: false - range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - smoker: - name: smoker - description: Specification of smoking status - title: smoker + hysterectomy: + name: hysterectomy + description: Specification of whether hysterectomy was performed + title: hysterectomy examples: - - value: 'yes' + - value: 'no' from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000262 + slot_uri: MIXS:0000287 multivalued: false range: boolean required: false recommended: false - sodium: - name: sodium + ihmc_medication_code: + name: ihmc_medication_code + description: Can include multiple medication codes + title: IHMC medication code + examples: + - value: '810' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - code + slot_uri: MIXS:0000884 + multivalued: true + range: integer + required: false + recommended: false + indoor_space: + name: indoor_space + description: A distinguishable space within a structure, the purpose for which + discrete areas of a building is used + title: indoor space + examples: + - value: foyer + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - indoor + slot_uri: MIXS:0000763 + multivalued: false + range: INDOOR_SPACE_ENUM + required: true + indoor_surf: + name: indoor_surf + description: Type of indoor surface + title: indoor surface + examples: + - value: wall + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - indoor + - surface + slot_uri: MIXS:0000764 + multivalued: false + range: INDOOR_SURF_ENUM + indust_eff_percent: + name: indust_eff_percent annotations: Preferred_unit: tag: Preferred_unit - value: milligram per liter, parts per million - description: Sodium concentration in the sample - title: sodium - examples: - - value: 10.5 milligram per liter + value: percentage + description: Percentage of industrial effluents received by wastewater treatment + plant + title: industrial effluent percent from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000428 + keywords: + - percent + slot_uri: MIXS:0000662 multivalued: false range: string required: false @@ -14611,19 +12557,40 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - soil_conductivity: - name: soil_conductivity + inorg_particles: + name: inorg_particles annotations: + Expected_value: + tag: Expected_value + value: inorganic particle name;measurement value Preferred_unit: tag: Preferred_unit - value: milliSiemens per centimeter - title: soil conductivity - examples: - - value: 10 milliSiemens per centimeter + value: mole per liter, milligram per liter + description: Concentration of particles such as sand, grit, metal particles, ceramics, + etc.; can include multiple particles + title: inorganic particles from_schema: https://w3id.org/mixs-6-2-rc keywords: - - soil - slot_uri: MIXS:0001158 + - inorganic + - particle + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000664 + multivalued: true + required: false + recommended: false + inside_lux: + name: inside_lux + annotations: + Preferred_unit: + tag: Preferred_unit + value: kilowatt per square metre + description: The recorded value at sampling time (power density) + title: inside lux light + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - inside + - light + slot_uri: MIXS:0000168 multivalued: false range: string required: false @@ -14634,282 +12601,276 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - soil_cover: - name: soil_cover - annotations: - Expected_value: - tag: Expected_value - value: subclass of 'environmental material', http://purl.obolibrary.org/obo/ENVO_00010483 - description: Material covering the sampled soil. This field accepts terms under - ENVO:00010483, environmental material - title: soil cover - examples: - - value: bare soil [ENVO01001616] - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - soil - string_serialization: bare soil [ENVO:01001616] - slot_uri: MIXS:0001159 - multivalued: false - soil_horizon: - name: soil_horizon - description: Specific layer in the land area which measures parallel to the soil - surface and possesses physical characteristics which differ from the layers - above and beneath - title: soil horizon + int_wall_cond: + name: int_wall_cond + description: The physical condition of the wall at the time of sampling; photos + or video preferred; use drawings to indicate location of damaged areas + title: interior wall condition examples: - - value: A horizon + - value: damaged from_schema: https://w3id.org/mixs-6-2-rc keywords: - - horizon - - soil - slot_uri: MIXS:0001082 + - condition + - interior + - wall + slot_uri: MIXS:0000813 multivalued: false - range: SOIL_HORIZON_ENUM - soil_pH: - name: soil_pH - title: soil pH - examples: - - value: '7.2' - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - ph - - soil - slot_uri: MIXS:0001160 - range: float + range: SHARED_ENUM_3 required: false recommended: false - soil_porosity: - name: soil_porosity + intended_consumer: + name: intended_consumer annotations: Expected_value: tag: Expected_value - value: percent porosity - Preferred_unit: - tag: Preferred_unit - value: percentage - description: Porosity of soil or deposited sediment is volume of voids divided - by the total volume of sample - title: soil sediment porosity + value: FOODON_03510136 or NCBI taxid + description: Food consumer type, human or animal, for which the food product is + produced and marketed. This field accepts terms listed under food consumer group + (http://purl.obolibrary.org/obo/FOODON_03510136) or NCBI taxid + title: intended consumer examples: - - value: '0.2' + - value: 9606 o rsenior as food consumer [FOODON:03510254] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - porosity - - sediment - - soil - string_serialization: '{percentage}' - slot_uri: MIXS:0001162 - multivalued: false - required: false - recommended: false - soil_temp: - name: soil_temp - annotations: - Preferred_unit: - tag: Preferred_unit - value: degree Celsius - description: Temperature of soil at the time of sampling - title: soil temperature + - consumer + string_serialization: '{integer}|{termLabel} [{termID}]' + slot_uri: MIXS:0001144 + multivalued: true + isol_growth_condt: + name: isol_growth_condt + description: Publication reference in the form of pubmed ID (pmid), digital object + identifier (doi) or url for isolation and growth condition specifications of + the organism/material + title: isolation and growth condition examples: - - value: 25 degrees Celsius + - value: doi:10.1016/j.syapm.2018.01.009 + in_subset: + - nucleic acid sequence source from_schema: https://w3id.org/mixs-6-2-rc keywords: - - soil - - temperature - slot_uri: MIXS:0001163 + - condition + - growth + - isolation + slot_uri: MIXS:0000003 multivalued: false range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: ^{PMID}|{DOI}|{URL}$ interpolated: true partial_match: true - soil_texture: - name: soil_texture - description: The relative proportion of different grain sizes of mineral particles - in a soil, as described using a standard system; express as % sand (50 um to - 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty - clay loam) optional - title: soil texture + iw_bt_date_well: + name: iw_bt_date_well + description: Injection water breakthrough date per well following a secondary + and/or tertiary recovery + title: injection water breakthrough date of specific well + examples: + - value: '2013-03-25T12:42:31+01:00' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - soil - - texture - slot_uri: MIXS:0000335 + - date + - water + slot_uri: MIXS:0001010 multivalued: false - range: string + range: datetime required: false recommended: false + iwf: + name: iwf + annotations: + Preferred_unit: + tag: Preferred_unit + value: percent + description: Proportion of the produced fluids derived from injected water at + the time of sampling. (e.g. 87%) + title: injection water fraction + comments: + - pattern was "[0-9]*\\.?[0-9]+ ?%" + - percent or float? + examples: + - value: '0.79' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - fraction + - water + slot_uri: MIXS:0000455 + range: float + required: true pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - soil_texture_class: - name: soil_texture_class - description: One of the 12 soil texture classes use to describe soil texture based - on the relative proportion of different grain sizes of mineral particles [sand - (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um)] in a soil - title: soil texture classification - examples: - - value: silty clay loam + kidney_disord: + name: kidney_disord + description: History of kidney disorders; can include multiple disorders. The + terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + kidney disease (https://disease-ontology.org/?id=DOID:557) + title: urine/kidney disorder from_schema: https://w3id.org/mixs-6-2-rc keywords: - - classification - - soil - - texture - slot_uri: MIXS:0001164 - multivalued: false - range: SOIL_TEXTURE_CLASS_ENUM + - disorder + slot_uri: MIXS:0000277 + multivalued: true + range: string required: false recommended: false - soil_texture_meth: - name: soil_texture_meth - description: Reference or method used in determining soil texture - title: soil texture method + last_clean: + name: last_clean + description: The last time the floor was cleaned (swept, mopped, vacuumed) + title: last time swept/mopped/vacuumed examples: - - value: https://uwlab.soils.wisc.edu/wp-content/uploads/sites/17/2015/09/particle_size.pdf + - value: '2013-03-25T12:42:31+01:00' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - method - - soil - - texture - slot_uri: MIXS:0000336 + - time + slot_uri: MIXS:0000814 multivalued: false - range: string + range: datetime required: false recommended: false - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ - structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ - interpolated: true - partial_match: true - soil_type: - name: soil_type + lat_lon: + name: lat_lon annotations: Expected_value: tag: Expected_value - value: ENVO:00001998 - description: Description of the soil type or classification. This field accepts - terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms - can be separated by pipes - title: soil type + value: decimal degrees, limit to 8 decimal points + description: The geographical origin of the sample as defined by latitude and + longitude. The values should be reported in decimal degrees and in WGS84 system + title: geographic location (latitude and longitude) examples: - - value: plinthosol [ENVO:00002250] + - value: 50.586825 6.408977 + in_subset: + - environment from_schema: https://w3id.org/mixs-6-2-rc keywords: - - soil - - type - slot_uri: MIXS:0000332 - multivalued: false - soil_type_meth: - name: soil_type_meth - description: Reference or method used in determining soil series name or other - lower-level classification - title: soil type method + - geographic + - location + string_serialization: '{float} {float}' + slot_uri: MIXS:0000009 + required: true + pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$ + structured_pattern: + syntax: ^{lat} {lon}$ + interpolated: true + partial_match: true + lib_layout: + name: lib_layout + description: Specify whether to expect single, paired, or other configuration + of reads + title: library layout examples: - - value: https://www.lrh.usace.army.mil/Portals/38/docs/PR/BluestoneSFEIS/Appendix%20K-Soil%20Descriptions.pdf + - value: paired + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - method - - soil - - type - slot_uri: MIXS:0000334 + - library + slot_uri: MIXS:0000041 multivalued: false - range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ - structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ - interpolated: true - partial_match: true - solar_irradiance: - name: solar_irradiance - annotations: - Preferred_unit: - tag: Preferred_unit - value: kilowatts per square meter per day, ergs per square centimeter per - second - description: The amount of solar energy that arrives at a specific area of a surface - during a specific time interval - title: solar irradiance + range: LIB_LAYOUT_ENUM + lib_reads_seqd: + name: lib_reads_seqd + description: Total number of clones sequenced from the library + title: library reads sequenced examples: - - value: 1.36 kilowatts per square meter per day + - value: '20' + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000112 - multivalued: true - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - soluble_inorg_mat: - name: soluble_inorg_mat + keywords: + - library + slot_uri: MIXS:0000040 + multivalued: false + range: integer + lib_screen: + name: lib_screen annotations: Expected_value: tag: Expected_value - value: soluble inorganic material name;measurement value - Preferred_unit: - tag: Preferred_unit - value: gram, microgram, mole per liter, gram per liter, parts per million - description: Concentration of substances such as ammonia, road-salt, sea-salt, - cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc - title: soluble inorganic material - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - inorganic - - material - - soluble - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000672 - multivalued: true - required: false - recommended: false - soluble_org_mat: - name: soluble_org_mat + value: screening strategy name + description: Specific enrichment or screening methods applied before and/or after + creating libraries + title: library screening strategy + examples: + - value: enriched, screened, normalized + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - library + string_serialization: '{text}' + slot_uri: MIXS:0000043 + multivalued: false + lib_size: + name: lib_size + description: Total number of clones in the library prepared for the project + title: library size + examples: + - value: '50' + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - library + - size + slot_uri: MIXS:0000039 + multivalued: false + range: integer + lib_vector: + name: lib_vector annotations: Expected_value: tag: Expected_value - value: soluble organic material name;measurement value - Preferred_unit: - tag: Preferred_unit - value: gram, microgram, mole per liter, gram per liter, parts per million - description: Concentration of substances such as urea, fruit sugars, soluble proteins, - drugs, pharmaceuticals, etc - title: soluble organic material + value: vector + description: Cloning vector type(s) used in construction of libraries + title: library vector + examples: + - value: Bacteriophage P1 + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - material - - organic - - soluble - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000673 - multivalued: true + - library + string_serialization: '{text}' + slot_uri: MIXS:0000042 + multivalued: false + library_prep_kit: + name: library_prep_kit + annotations: + Expected_value: + tag: Expected_value + value: name of library preparation kit + description: Packaged kits (containing adapters, indexes, enzymes, buffers etc.), + tailored for specific sequencing workflows, which allow the simplified preparation + of sequencing-ready libraries for small genomes, amplicons, and plasmids + title: library preparation kit + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - kit + - library + - preparation + string_serialization: '{text}' + slot_uri: MIXS:0001145 + multivalued: false required: false recommended: false - soluble_react_phosp: - name: soluble_react_phosp + light_intensity: + name: light_intensity annotations: Preferred_unit: tag: Preferred_unit - value: micromole per liter, milligram per liter, parts per million - description: Concentration of soluble reactive phosphorus - title: soluble reactive phosphorus + value: lux + description: Measurement of light intensity + title: light intensity examples: - - value: 0.1 milligram per liter + - value: 0.3 lux from_schema: https://w3id.org/mixs-6-2-rc keywords: - - phosphorus - - soluble - slot_uri: MIXS:0000738 + - intensity + - light + slot_uri: MIXS:0000706 multivalued: false range: string required: false @@ -14920,590 +12881,488 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - sop: - name: sop + light_regm: + name: light_regm annotations: Expected_value: tag: Expected_value - value: reference to SOP - description: Standard operating procedures used in assembly and/or annotation - of genomes, metagenomes or environmental sequences - title: relevant standard operating procedures + value: exposure type;light intensity;light quality + Preferred_unit: + tag: Preferred_unit + value: lux; micrometer, nanometer, angstrom + description: Information about treatment(s) involving exposure to light, including + both light intensity and quality + title: light regimen examples: - - value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ - in_subset: - - sequencing + - value: incandescant light;10 lux;450 nanometer from_schema: https://w3id.org/mixs-6-2-rc keywords: - - procedures - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000090 - multivalued: true - sort_tech: - name: sort_tech - description: Method used to sort/isolate cells or particles of interest - title: sorting technology - examples: - - value: optical manipulation - in_subset: - - sequencing - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000075 + - light + - regimen + string_serialization: '{text};{float} {unit};{float} {unit}' + slot_uri: MIXS:0000569 multivalued: false - range: SORT_TECH_ENUM - source_mat_id: - name: source_mat_id - annotations: - Expected_value: - tag: Expected_value - value: 'for cultures of microorganisms: identifiers for two culture collections; - for other material a unique arbitrary identifer' - description: A unique identifier assigned to a material sample (as defined by - http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular - digital record of a material sample) used for extracting nucleic acids, and - subsequent sequencing. The identifier can refer either to the original material - collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, - /bio_material, or /culture_collection may or may not share the same value as - the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id - may both contain 'UAM:Herps:14' , referring to both the specimen voucher and - sampled tissue with the same identifier. However, the /culture_collection qualifier - may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id - would refer to an identifier from some derived culture from which the nucleic - acids were extracted (e.g. xatc123 or ark:/2154/R2) - title: source material identifiers + required: false + recommended: false + light_type: + name: light_type + description: Application of light to achieve some practical or aesthetic effect. + Lighting includes the use of both artificial light sources such as lamps and + light fixtures, as well as natural illumination by capturing daylight. Can also + include absence of light + title: light type examples: - - value: MPI012345 - in_subset: - - nucleic acid sequence source + - value: desk lamp from_schema: https://w3id.org/mixs-6-2-rc keywords: - - identifier - - material - - source - string_serialization: '{text}' - slot_uri: MIXS:0000026 + - light + - type + slot_uri: MIXS:0000769 multivalued: true - source_uvig: - name: source_uvig - annotations: - Expected_value: - tag: Expected_value - value: enumeration - description: Type of dataset from which the UViG was obtained - title: source of UViGs - examples: - - value: viral fraction metagenome (virome) - in_subset: - - nucleic acid sequence source - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - source - string_serialization: '[metagenome (not viral targeted)|viral fraction metagenome - (virome)|sequence-targeted metagenome|metatranscriptome (not viral targeted)|viral - fraction RNA metagenome (RNA virome)|sequence-targeted RNA metagenome|microbial - single amplified genome (SAG)|viral single amplified genome (vSAG)|isolate microbial - genome|other]' - slot_uri: MIXS:0000035 - multivalued: false - space_typ_state: - name: space_typ_state - description: Customary or normal state of the space - title: space typical state - examples: - - value: typically occupied - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000770 - multivalued: false - range: SPACE_TYP_STATE_ENUM + range: LIGHT_TYPE_ENUM required: true - spec_intended_cons: - name: spec_intended_cons - description: Food consumer type, human or animal, for which the food product is - produced and marketed. This field accepts terms listed under food consumer group - (http://purl.obolibrary.org/obo/FOODON_03510136) - title: specific intended consumer - examples: - - value: senior as food consumer [FOODON:03510254] + link_addit_analys: + name: link_addit_analys + description: Link to additional analysis results performed on the sample + title: links to additional analysis from_schema: https://w3id.org/mixs-6-2-rc keywords: - - consumer - slot_uri: MIXS:0001234 - multivalued: true + - link + slot_uri: MIXS:0000340 + multivalued: false range: string required: false recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ structured_pattern: - syntax: ^{termLabel} \[{termID}\]$ + syntax: ^{PMID}|{DOI}|{URL}$ interpolated: true partial_match: true - special_diet: - name: special_diet + link_class_info: + name: link_class_info annotations: Expected_value: tag: Expected_value - value: enumeration - description: Specification of special diet; can include multiple special diets - title: special diet - examples: - - value: other:vegan + value: PMID,DOI or url + description: Link to digitized soil maps or other soil classification information + title: link to classification information from_schema: https://w3id.org/mixs-6-2-rc keywords: - - diet - string_serialization: '[low carb|reduced calorie|vegetarian|other(to be specified)]' - slot_uri: MIXS:0000905 - multivalued: true + - classification + - information + - link + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0000329 + multivalued: false required: false recommended: false - specific: - name: specific - description: 'The building specifications. If design is chosen, indicate phase: - conceptual, schematic, design development, construction documents' - title: specifications + link_climate_info: + name: link_climate_info + description: Link to climate resource + title: link to climate information + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - information + - link + slot_uri: MIXS:0000328 + multivalued: false + range: string + required: false + recommended: false + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + lithology: + name: lithology + description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). + If "other" is specified, please propose entry in "additional info" field' + title: lithology examples: - - value: construction + - value: Volcanic from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000836 + keywords: + - lithology + slot_uri: MIXS:0000990 multivalued: false - range: SPECIFIC_ENUM + range: LITHOLOGY_ENUM + recommended: true + liver_disord: + name: liver_disord + description: History of liver disorders; can include multiple disorders. The terms + should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + liver disease (https://disease-ontology.org/?id=DOID:409) + title: liver disorder + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - disorder + slot_uri: MIXS:0000282 + multivalued: true + range: string required: false recommended: false - specific_host: - name: specific_host + local_class: + name: local_class annotations: Expected_value: tag: Expected_value - value: host scientific name, taxonomy ID - description: Report the host's taxonomic name and/or NCBI taxonomy ID - title: host scientific name - examples: - - value: Homo sapiens and/or 9606 - in_subset: - - nucleic acid sequence source + value: local classification name + description: Soil classification based on local soil classification system + title: soil_taxonomic/local classification from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - string_serialization: '{text}|{NCBI taxid}' - slot_uri: MIXS:0000029 + - classification + string_serialization: '{text}' + slot_uri: MIXS:0000330 multivalued: false - specific_humidity: - name: specific_humidity - annotations: - Preferred_unit: - tag: Preferred_unit - value: gram of air, kilogram of air - description: The mass of water vapour in a unit mass of moist air, usually expressed - as grams of vapour per kilogram of air, or, in air conditioning, as grains per - pound - title: specific humidity - examples: - - value: 15 per kilogram of air + local_class_meth: + name: local_class_meth + description: Reference or method used in determining the local soil classification + title: soil_taxonomic/local classification method from_schema: https://w3id.org/mixs-6-2-rc keywords: - - humidity - slot_uri: MIXS:0000214 + - classification + - method + slot_uri: MIXS:0000331 multivalued: false range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: ^{PMID}|{DOI}|{URL}$ interpolated: true partial_match: true - spikein_AMR: - name: spikein_AMR + lot_number: + name: lot_number annotations: Expected_value: tag: Expected_value - value: measurement value ARO:3004299 - description: Qualitative description of a microbial response to antimicrobial - agents. Bacteria may be susceptible or resistant to a broad range of antibiotic - drugs or drug classes, with several intermediate states or phases. This field - accepts terms under antimicrobial phenotype (http://purl.obolibrary.org/obo/ARO_3004299) - title: antimicrobial phenotype of spike-in bacteria + value: lot number, item + description: 'A distinctive alpha-numeric identification code assigned by the + manufacturer or distributor to a specific quantity of manufactured material + or product within a batch. Synonym: Batch Number. The submitter should provide + lot number of the item followed by the item name for which the lot number was + provided' + title: lot number examples: - - value: wild type [ARO:3004432] + - value: 1239ABC01A, split Cornish hens from_schema: https://w3id.org/mixs-6-2-rc keywords: - - antimicrobial - - spike - string_serialization: '{float} {unit};{termLabel} [{termID}]' - slot_uri: MIXS:0001235 + - number + string_serialization: '{integer}, {text}' + slot_uri: MIXS:0001147 multivalued: true required: false recommended: false - spikein_antibiotic: - name: spikein_antibiotic - annotations: - Expected_value: - tag: Expected_value - value: drug name; concentration - description: Antimicrobials used in research study to assess effects of exposure - on microbiome of a specific site. Please list antimicrobial, common name and/or - class and concentration used for spike-in - title: spike-in with antibiotics + mag_cov_software: + name: mag_cov_software + description: Tool(s) used to determine the genome coverage if coverage is used + as a binning parameter in the extraction of genomes from metagenomic datasets + title: MAG coverage software examples: - - value: Tetracycline at 5 mg/ml + - value: bbmap + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - spike - string_serialization: '{text} {integer}' - slot_uri: MIXS:0001171 - multivalued: true - required: false - recommended: false - spikein_count: - name: spikein_count + - software + slot_uri: MIXS:0000080 + multivalued: false + range: MAG_COV_SOFTWARE_ENUM + magnesium: + name: magnesium annotations: - Expected_value: - tag: Expected_value - value: organism name;measurement value;enumeration Preferred_unit: tag: Preferred_unit - value: colony forming units per milliliter; colony forming units per gram - of dry weight - description: 'Total cell count of any organism (or group of organisms) per gram, - volume or area of sample, should include name of organism followed by count. - The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) should - also be provided (example: total prokaryotes; 3.5e7 cells per ml; qPCR)' - title: spike-in organism count + value: mole per liter, milligram per liter, parts per million, micromole per + kilogram + description: Concentration of magnesium in the sample + title: magnesium examples: - - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR + - value: 52.8 micromole per kilogram from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - count - - organism - - spike - string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]' - slot_uri: MIXS:0001335 + slot_uri: MIXS:0000431 multivalued: false - required: false - recommended: false - spikein_growth_med: - name: spikein_growth_med - description: A liquid or gel containing nutrients, salts, and other factors formulated - to support the growth of microorganisms, cells, or plants (National Cancer Institute - Thesaurus). A growth medium is a culture medium which has the disposition to - encourage growth of particular bacteria to the exclusion of others in the same - growth environment. In this case, list the culture medium used to propagate - the spike-in bacteria during preparation of spike-in inoculum. This field accepts - terms listed under microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067). - If the proper descriptor is not listed please use text to describe the spike - in growth media - title: spike-in growth medium - examples: - - value: LB broth [MCO:0000036] - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - growth - - spike - slot_uri: MIXS:0001169 - multivalued: true range: string required: false recommended: false - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$ + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{text}|({termLabel} \[{termID}\])$ + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - spikein_metal: - name: spikein_metal - annotations: - Expected_value: - tag: Expected_value - value: heavy metal name or chemical symbol; concentration - description: Heavy metals used in research study to assess effects of exposure - on microbiome of a specific site. Please list heavy metals and concentration - used for spike-in - title: spike-in with heavy metals - examples: - - value: Cd at 20 ppm + maternal_health_stat: + name: maternal_health_stat + description: Specification of the maternal health status + title: amniotic fluid/maternal health status from_schema: https://w3id.org/mixs-6-2-rc keywords: - - heavy - - spike - string_serialization: '{text} {integer}' - slot_uri: MIXS:0001172 - multivalued: true + - status + slot_uri: MIXS:0000273 + multivalued: false + range: string required: false recommended: false - spikein_org: - name: spikein_org - description: Taxonomic information about the spike-in organism(s). This field - accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This - field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. - Multiple terms can be separated by pipes - title: spike in organism - examples: - - value: Listeria monocytogenes [NCIT:C86502]|28901 + max_occup: + name: max_occup + description: The maximum amount of people allowed in the indoor environment + title: maximum occupancy from_schema: https://w3id.org/mixs-6-2-rc keywords: - - organism - - spike - slot_uri: MIXS:0001167 - multivalued: true + - maximum + slot_uri: MIXS:0000229 + multivalued: false range: string required: false recommended: false - pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^({termLabel} \[{termID}\])|{integer}$ + syntax: ^{integer} {text}$ interpolated: true partial_match: true - spikein_serovar: - name: spikein_serovar - annotations: - Expected_value: - tag: Expected_value - value: NCIT:C14250 or antigenic formula or serovar name - description: Taxonomic information about the spike-in organism(s) at the serovar - or serotype level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). - This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. - Multiple terms can be separated by pipes - title: spike-in bacterial serovar or serotype + mean_frict_vel: + name: mean_frict_vel + annotations: + Preferred_unit: + tag: Preferred_unit + value: meter per second + description: Measurement of mean friction velocity + title: mean friction velocity examples: - - value: Escherichia coli strain O157:H7 [NCIT:C86883]|83334 + - value: 0.5 meter per second from_schema: https://w3id.org/mixs-6-2-rc keywords: - - spike - string_serialization: '{termLabel} [{termID}]|{integer}' - slot_uri: MIXS:0001168 - multivalued: true + - mean + - velocity + slot_uri: MIXS:0000498 + multivalued: false + range: string required: false recommended: false - spikein_strain: - name: spikein_strain + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + mean_peak_frict_vel: + name: mean_peak_frict_vel + annotations: + Preferred_unit: + tag: Preferred_unit + value: meter per second + description: Measurement of mean peak friction velocity + title: mean peak friction velocity + examples: + - value: 1 meter per second + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - mean + - peak + - velocity + slot_uri: MIXS:0000502 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + mech_struc: + name: mech_struc + description: 'mechanical structure: a moving structure' + title: mechanical structure + examples: + - value: elevator + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000815 + multivalued: false + range: MECH_STRUC_ENUM + required: false + recommended: false + mechanical_damage: + name: mechanical_damage annotations: Expected_value: tag: Expected_value - value: NCIT:C14250 or NCBI taxid or text - description: Taxonomic information about the spike-in organism(s) at the strain - level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). - This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. - Multiple terms can be separated by pipes - title: spike-in microbial strain + value: damage type;body site + description: Information about any mechanical damage exerted on the plant; can + include multiple damages and sites + title: mechanical damage examples: - - value: '169963' + - value: pruning;bark from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - microbial - - spike - string_serialization: '{termLabel} [{termID}]|{integer}' - slot_uri: MIXS:0001170 + string_serialization: '{text};{text}' + slot_uri: MIXS:0001052 multivalued: true required: false recommended: false - sr_dep_env: - name: sr_dep_env - description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). - If "other" is specified, please propose entry in "additional info" field - title: source rock depositional environment + medic_hist_perform: + name: medic_hist_perform + description: Whether full medical history was collected + title: medical history performed examples: - - value: Marine + - value: '1' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - environment - - source - slot_uri: MIXS:0000996 + - history + slot_uri: MIXS:0000897 multivalued: false - range: SR_DEP_ENV_ENUM + range: boolean required: false recommended: false - sr_geol_age: - name: sr_geol_age - description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). - If "other" is specified, please propose entry in "additional info" field' - title: source rock geological age + menarche: + name: menarche + description: Date of most recent menstruation + title: menarche examples: - - value: Silurian + - value: '2013-03-25T12:42:31+01:00' from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - age - - source - slot_uri: MIXS:0000997 + slot_uri: MIXS:0000965 multivalued: false - range: SHARED_ENUM_5 + range: datetime required: false recommended: false - sr_kerog_type: - name: sr_kerog_type - description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic - and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ - fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris - (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). - If "other" is specified, please propose entry in "additional info" field' - title: source rock kerogen type + menopause: + name: menopause + description: Date of onset of menopause + title: menopause examples: - - value: Type IV + - value: '2013-03-25T12:42:31+01:00' from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - source - - type - slot_uri: MIXS:0000994 + slot_uri: MIXS:0000968 multivalued: false - range: SR_KEROG_TYPE_ENUM + range: datetime required: false recommended: false - sr_lithology: - name: sr_lithology - description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). - If "other" is specified, please propose entry in "additional info" field - title: source rock lithology - examples: - - value: Coal + methane: + name: methane + annotations: + Preferred_unit: + tag: Preferred_unit + value: micromole per liter, parts per billion, parts per million + description: Methane (gas) amount or concentration at the time of sampling + title: methane from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - lithology - - source - slot_uri: MIXS:0000995 + slot_uri: MIXS:0000101 multivalued: false - range: SR_LITHOLOGY_ENUM + range: string required: false recommended: false - standing_water_regm: - name: standing_water_regm - description: Treatment involving an exposure to standing water during a plant's - life span, types can be flood water or standing water, treatment regimen including - how many times the treatment was repeated, how long each treatment lasted, and - the start and end time of the entire treatment; can include multiple regimens - title: standing water regimen + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + micro_biomass_meth: + name: micro_biomass_meth + description: Reference or method used in determining microbial biomass + title: microbial biomass method + comments: + - slot name/scn was microbial_biomass_meth examples: - - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: http://dx.doi.org/10.1016/j.soilbio.2005.01.021 from_schema: https://w3id.org/mixs-6-2-rc keywords: - - regimen - - water - slot_uri: MIXS:0001069 - multivalued: true + - biomass + - method + - microbial + slot_uri: MIXS:0000339 range: string - ster_meth_samp_room: - name: ster_meth_samp_room - annotations: - Expected_value: - tag: Expected_value - value: ENVO:01001026 - description: The method used to sterilize the sampling room. This field accepts - terms listed under electromagnetic radiation (http://purl.obolibrary.org/obo/ENVO_01001026). - If the proper descriptor is not listed, please use text to describe the sampling - room sterilization method. Multiple terms can be separated by pipes - title: sampling room sterilization method + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + microb_cult_med: + name: microb_cult_med + description: A culture medium used to select for, grow, and maintain prokaryotic + microorganisms. Can be in either liquid (broth) or solidified (e.g. with agar) + forms. This field accepts terms listed under microbiological culture medium + (http://purl.obolibrary.org/obo/MICRO_0000067). If the proper descriptor is + not listed please use text to describe the culture medium + title: microbiological culture medium examples: - - value: ultraviolet radiation [ENVO:21001216]|infrared radiation [ENVO:21001214] + - value: brain heart infusion agar [MICRO:0000566] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - method - - room - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001259 - multivalued: true + - culture + - microbiological + slot_uri: MIXS:0001216 + multivalued: false + range: string required: false recommended: false - store_cond: - name: store_cond + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$ + structured_pattern: + syntax: ^{text}|({termLabel} \[{termID}\])$ + interpolated: true + partial_match: true + microb_start: + name: microb_start annotations: Expected_value: tag: Expected_value - value: storage condition type;duration - description: Explain how and for how long the soil sample was stored before DNA - extraction (fresh/frozen/other) - title: storage conditions + value: FOODON:03544453 + description: Any type of microorganisms used in food production. This field accepts + terms listed under live organisms for food production (http://purl.obolibrary.org/obo/FOODON_0344453) + title: microbial starter examples: - - value: -20 degree Celsius freezer;P2Y10D - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - condition - - storage - string_serialization: '{text};{period}' - slot_uri: MIXS:0000327 - multivalued: false - study_complt_stat: - name: study_complt_stat - annotations: - Expected_value: - tag: Expected_value - value: YES or NO due to (1)adverse event (2) non-compliance (3) lost to follow - up (4)other-specify - description: Specification of study completion status, if no the reason should - be specified - title: study completion status - examples: - - value: no;non-compliance + - value: starter cultures [FOODON:03544454] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - status - string_serialization: '{boolean};[adverse event|non-compliance|lost to follow - up|other-specify]' - slot_uri: MIXS:0000898 + - microbial + string_serialization: '{term label} [{termID}]|{text}' + slot_uri: MIXS:0001217 multivalued: false required: false recommended: false - study_design: - name: study_design + microb_start_count: + name: microb_start_count annotations: Expected_value: tag: Expected_value - value: OBI:0500000 - description: A plan specification comprised of protocols (which may specify how - and what kinds of data will be gathered) that are executed as part of an investigation - and is realized during a study design execution. This field accepts terms under - study design (http://purl.obolibrary.org/obo/OBI_0500000). If the proper descriptor - is not listed please use text to describe the study design. Multiple terms can - be separated by pipes - title: study design - examples: - - value: in vitro design [OBI:0001285] - from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001236 - multivalued: true - required: false - recommended: false - study_inc_dur: - name: study_inc_dur - annotations: + value: organism name; measurement value; enumeration Preferred_unit: tag: Preferred_unit - value: hours or days - description: Sample incubation duration if unpublished or unvalidated method is - used. Indicate the timepoint written in ISO 8601 format - title: study incubation duration + value: colony forming units per milliliter; colony forming units per gram + of dry weight + description: 'Total cell count of starter culture per gram, volume or area of + sample and the method that was used for the enumeration (e.g. qPCR, atp, mpn, + etc.) should also be provided. (example : total prokaryotes; 3.5e7 cells per + ml; qPCR)' + title: microbial starter organism count examples: - - value: PT24H + - value: total prokaryotes;3.5e9 colony forming units per milliliter;spread plate from_schema: https://w3id.org/mixs-6-2-rc keywords: - - duration - - incubation - - period - slot_uri: MIXS:0001237 + - count + - microbial + - organism + string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|spread plate|other]' + slot_uri: MIXS:0001218 multivalued: false - range: string required: false recommended: false - pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ - structured_pattern: - syntax: ^{duration}$ - interpolated: true - partial_match: true - study_inc_temp: - name: study_inc_temp + microb_start_inoc: + name: microb_start_inoc annotations: Preferred_unit: tag: Preferred_unit - value: degree Celsius - description: Sample incubation temperature if unpublished or unvalidated method - is used - title: study incubation temperature + value: milligram or gram + description: The amount of starter culture used to inoculate a new batch + title: microbial starter inoculation examples: - - value: 37 degree Celsius + - value: 100 milligrams from_schema: https://w3id.org/mixs-6-2-rc keywords: - - incubation - - temperature - slot_uri: MIXS:0001238 + - microbial + slot_uri: MIXS:0001219 multivalued: false range: string required: false @@ -15514,108 +13373,77 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - study_timecourse: - name: study_timecourse - annotations: - Preferred_unit: - tag: Preferred_unit - value: dpi - description: For time-course research studies involving samples of the food commodity, - indicate the total duration of the time-course study - title: time-course duration + microb_start_prep: + name: microb_start_prep + description: Information about the protocol or method used to prepare the starter + inoculum + title: microbial starter preparation examples: - - value: 2 days post inoculation + - value: liquid starter culture, propagated 3 cycles in milk prior to inoculation from_schema: https://w3id.org/mixs-6-2-rc keywords: - - duration - - period - - time - slot_uri: MIXS:0001239 + - microbial + - preparation + slot_uri: MIXS:0001220 multivalued: false range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - study_tmnt: - name: study_tmnt - annotations: - Expected_value: - tag: Expected_value - value: MCO:0000866 - description: A process in which the act is intended to modify or alter some other - material entity. From the study design, each treatment is comprised of one - level of one or multiple factors. This field accepts terms listed under treatment - (http://purl.obolibrary.org/obo/MCO_0000866). If the proper descriptor is not - listed please use text to describe the study treatment. Multiple terms can be - separated by one or more pipes - title: study treatment + microb_start_source: + name: microb_start_source + description: The source from which the microbial starter culture was sourced. If + commercially supplied, list supplier + title: microbial starter source examples: - - value: Factor A|spike-in|levels high, medium, low + - value: backslopped, GetCulture from_schema: https://w3id.org/mixs-6-2-rc keywords: - - treatment - string_serialization: '{text}|{termLabel} [{termID}]' - slot_uri: MIXS:0001240 - multivalued: true + - microbial + - source + slot_uri: MIXS:0001221 + multivalued: false + range: string required: false recommended: false - subspecf_gen_lin: - name: subspecf_gen_lin - annotations: - Expected_value: - tag: Expected_value - value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, - e.g. serovar, biotype, ecotype, variety, cultivar - description: Information about the genetic distinctness of the sequenced organism - below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any - relevant genetic typing schemes like Group I plasmid. Subspecies should not - be recorded in this term, but in the NCBI taxonomy. Supply both the lineage - name and the lineage rank separated by a colon, e.g., biovar:abc123 - title: subspecific genetic lineage + microb_start_taxID: + name: microb_start_taxID + description: Please include Genus species and strain ID, if known of microorganisms + used in food production. For complex communities, pipes can be used to separate + two or more microbes + title: microbial starter NCBI taxonomy ID examples: - - value: serovar:Newport - in_subset: - - nucleic acid sequence source + - value: Lactobacillus rhamnosus [NCIT:C123495] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - lineage - string_serialization: '{rank name}:{text}' - slot_uri: MIXS:0000020 + - identifier + - microbial + - ncbi + - taxon + slot_uri: MIXS:0001222 multivalued: false - substructure_type: - name: substructure_type - description: The substructure or under building is that largely hidden section - of the building which is built off the foundations to the ground floor level - title: substructure type - examples: - - value: basement - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - type - slot_uri: MIXS:0000767 - multivalued: true - range: SUBSTRUCTURE_TYPE_ENUM + range: string required: false recommended: false - sulfate: - name: sulfate + pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ + structured_pattern: + syntax: ^({termLabel} \[{termID}\])|{integer}$ + interpolated: true + partial_match: true + microbial_biomass: + name: microbial_biomass annotations: Preferred_unit: tag: Preferred_unit - value: micromole per liter, milligram per liter, parts per million - description: Concentration of sulfate in the sample - title: sulfate - examples: - - value: 5 micromole per liter + value: ton, kilogram, gram per kilogram soil + description: The part of the organic matter in the soil that constitutes living + microorganisms smaller than 5-10 micrometer. If you keep this, you would need + to have correction factors used for conversion to the final units + title: microbial biomass from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sulfate - slot_uri: MIXS:0000423 + - biomass + - microbial + slot_uri: MIXS:0000650 multivalued: false range: string pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? @@ -15624,177 +13452,176 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - sulfate_fw: - name: sulfate_fw - annotations: - Preferred_unit: - tag: Preferred_unit - value: milligram per liter - description: Original sulfate concentration in the hydrocarbon resource - title: sulfate in formation water + mid: + name: mid + description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are + used to specifically tag unique samples in a sequencing run. Sequence should + be reported in uppercase letters + title: multiplex identifiers + examples: + - value: GTGAATAT + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sulfate - - water - slot_uri: MIXS:0000407 + - identifier + slot_uri: MIXS:0000047 multivalued: false range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^[ACGTRKSYMWBHDVN]+$ structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: ^{ambiguous_nucleotides}$ interpolated: true partial_match: true - sulfide: - name: sulfide + mineral_nutr_regm: + name: mineral_nutr_regm annotations: + Expected_value: + tag: Expected_value + value: mineral nutrient name;mineral nutrient amount;treatment interval and + duration Preferred_unit: tag: Preferred_unit - value: micromole per liter, milligram per liter, parts per million - description: Concentration of sulfide in the sample - title: sulfide + value: gram, mole per liter, milligram per liter + description: Information about treatment involving the use of mineral supplements; + should include the name of mineral nutrient, amount administered, treatment + regimen including how many times the treatment was repeated, how long each treatment + lasted, and the start and end time of the entire treatment; can include multiple + mineral nutrient regimens + title: mineral nutrient regimen examples: - - value: 2 micromole per liter + - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc keywords: - - sulfide - slot_uri: MIXS:0000424 - multivalued: false - range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - surf_air_cont: - name: surf_air_cont - description: Contaminant identified on surface - title: surface-air contaminant - examples: - - value: radon - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000759 + - mineral + - nutrient + - regimen + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000570 multivalued: true - range: SURF_AIR_CONT_ENUM - recommended: true - surf_humidity: - name: surf_humidity + required: false + recommended: false + misc_param: + name: misc_param annotations: - Preferred_unit: - tag: Preferred_unit - value: percentage - description: 'Surfaces: water activity as a function of air and material moisture' - title: surface humidity - comments: - - percent or float? + Expected_value: + tag: Expected_value + value: parameter name;measurement value + description: Any other measurement performed or parameter collected, that is not + listed here + title: miscellaneous parameter examples: - - value: '0.1' + - value: Bicarbonate ion concentration;2075 micromole per kilogram from_schema: https://w3id.org/mixs-6-2-rc keywords: - - humidity - - surface - slot_uri: MIXS:0000123 - range: float + - parameter + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000752 + multivalued: true + required: false + recommended: false + mode_transmission: + name: mode_transmission + description: The process through which the symbiotic host organism entered the + host from which it was sampled + title: mode of transmission + examples: + - value: horizontal:castrator + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0001312 + range: MODE_TRANSMISSION_ENUM recommended: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - surf_material: - name: surf_material - description: Surface materials at the point of sampling - title: surface material + n_alkanes: + name: n_alkanes + annotations: + Expected_value: + tag: Expected_value + value: n-alkane name;measurement value + description: Concentration of n-alkanes; can include multiple n-alkanes + title: n-alkanes examples: - - value: wood + - value: n-hexadecane;100 milligram per liter + from_schema: https://w3id.org/mixs-6-2-rc + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000503 + multivalued: true + required: false + recommended: false + neg_cont_type: + name: neg_cont_type + annotations: + Expected_value: + tag: Expected_value + value: enumeration or text + description: The substance or equipment used as a negative control in an investigation + title: negative control type + in_subset: + - investigation from_schema: https://w3id.org/mixs-6-2-rc keywords: - - material - - surface - slot_uri: MIXS:0000758 + - type + slot_uri: MIXS:0001321 multivalued: false - range: SURF_MATERIAL_ENUM - surf_moisture: - name: surf_moisture + range: NEG_CONT_TYPE_ENUM + recommended: true + nitrate: + name: nitrate annotations: Preferred_unit: tag: Preferred_unit - value: parts per million, gram per cubic meter, gram per square meter - description: Water held on a surface - title: surface moisture + value: micromole per liter, milligram per liter, parts per million + description: Concentration of nitrate in the sample + title: nitrate examples: - - value: 0.01 gram per square meter + - value: 65 micromole per liter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - moisture - - surface - slot_uri: MIXS:0000128 + - nitrate + slot_uri: MIXS:0000425 multivalued: false range: string - recommended: true pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - surf_moisture_ph: - name: surf_moisture_ph - description: ph measurement of surface - title: surface moisture pH - examples: - - value: '7' - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - moisture - - ph - - surface - slot_uri: MIXS:0000760 - multivalued: false - range: float - recommended: true - surf_temp: - name: surf_temp + nitrite: + name: nitrite annotations: Preferred_unit: tag: Preferred_unit - value: degree Celsius - description: Temperature of the surface at the time of sampling - title: surface temperature + value: micromole per liter, milligram per liter, parts per million + description: Concentration of nitrite in the sample + title: nitrite examples: - - value: 15 degree Celsius + - value: 0.5 micromole per liter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - surface - - temperature - slot_uri: MIXS:0000125 + - nitrite + slot_uri: MIXS:0000426 multivalued: false range: string - recommended: true pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - suspend_part_matter: - name: suspend_part_matter + nitro: + name: nitro annotations: Preferred_unit: tag: Preferred_unit - value: milligram per liter - description: Concentration of suspended particulate matter - title: suspended particulate matter + value: micromole per liter + description: Concentration of nitrogen (total) + title: nitrogen examples: - - value: 0.5 milligram per liter + - value: 4.2 micromole per liter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - particle - - particulate - - suspended - slot_uri: MIXS:0000741 + - nitrogen + slot_uri: MIXS:0000504 multivalued: false range: string required: false @@ -15805,409 +13632,329 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - suspend_solids: - name: suspend_solids + non_min_nutr_regm: + name: non_min_nutr_regm annotations: - Expected_value: - tag: Expected_value - value: suspended solid name;measurement value Preferred_unit: tag: Preferred_unit - value: gram, microgram, milligram per liter, mole per liter, gram per liter, - part per million - description: Concentration of substances including a wide variety of material, - such as silt, decaying plant and animal matter; can include multiple substances - title: suspended solids + value: gram, mole per liter, milligram per liter + description: Information about treatment involving the exposure of plant to non-mineral + nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral + nutrient, amount administered, treatment regimen including how many times the + treatment was repeated, how long each treatment lasted, and the start and end + time of the entire treatment; can include multiple non-mineral nutrient regimens + title: non-mineral nutrient regimen + examples: + - value: https://phylogenomics.me/protocols/16s-pcr-protocol/ from_schema: https://w3id.org/mixs-6-2-rc keywords: - - solids - - suspended - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000150 + - non-mineral + - nutrient + - regimen + slot_uri: MIXS:0000571 multivalued: true - required: false - recommended: false - sym_life_cycle_type: - name: sym_life_cycle_type - annotations: - Expected_value: - tag: Expected_value - value: type of life cycle of the symbiotic organism (host of the samples) - description: Type of life cycle of the symbiotic host species (the thing being - sampled). Simple life cycles occur within a single host, complex ones within - multiple different hosts over the course of their normal life cycle - title: symbiotic host organism life cycle type - examples: - - value: complex life cycle + range: string + nose_mouth_teeth_throat_disord: + name: nose_mouth_teeth_throat_disord + description: History of nose/mouth/teeth/throat disorders; can include multiple + disorders. The terms should be chosen from the DO (Human Disease Ontology) at + http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), + mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), + or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974) + title: nose/mouth/teeth/throat disorder from_schema: https://w3id.org/mixs-6-2-rc keywords: - - host - - host. - - life - - organism - - symbiosis - - type - slot_uri: MIXS:0001300 - multivalued: false - range: SYM_LIFE_CYCLE_TYPE_ENUM - required: true - symbiont_host_role: - name: symbiont_host_role - description: Role of the host in the life cycle of the symbiotic organism - title: host of the symbiont role - examples: - - value: intermediate - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - - symbiosis - slot_uri: MIXS:0001303 - multivalued: false - range: SYMBIONT_HOST_ROLE_ENUM - recommended: true - tan: - name: tan - annotations: - Preferred_unit: - tag: Preferred_unit - value: milligram per liter - description: 'Total Acid Number (TAN) is a measurement of acidity that is determined - by the amount of potassium hydroxide in milligrams that is needed to neutralize - the acids in one gram of oil. It is an important quality measurement of crude - oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)' - title: total acid number + - disorder + slot_uri: MIXS:0000283 + multivalued: true + range: string + required: false + recommended: false + nose_throat_disord: + name: nose_throat_disord + description: History of nose-throat disorders; can include multiple disorders, The + terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory + tract disease (https://disease-ontology.org/?id=DOID:974) + title: nose throat disorder from_schema: https://w3id.org/mixs-6-2-rc keywords: - - number - - total - slot_uri: MIXS:0000120 - multivalued: false + - disorder + slot_uri: MIXS:0000270 + multivalued: true range: string - recommended: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - target_gene: - name: target_gene - description: Targeted gene or locus name for marker gene studies - title: target gene + required: false + recommended: false + nucl_acid_amp: + name: nucl_acid_amp + description: A link to a literature reference, electronic resource or a standard + operating procedure (SOP), that describes the enzymatic amplification (PCR, + TMA, NASBA) of specific nucleic acids + title: nucleic acid amplification examples: - - value: 16S rRNA, 18S rRNA, nif, amoA, rpo + - value: https://phylogenomics.me/protocols/16s-pcr-protocol/ in_subset: - sequencing from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - target - slot_uri: MIXS:0000044 + slot_uri: MIXS:0000038 multivalued: false range: string - target_subfragment: - name: target_subfragment - description: Name of subfragment of a gene or locus. Important to e.g. identify - special regions on marker genes like V6 on 16S rRNA - title: target subfragment + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + nucl_acid_ext: + name: nucl_acid_ext + description: A link to a literature reference, electronic resource or a standard + operating procedure (SOP), that describes the material separation to recover + the nucleic acid fraction from a sample + title: nucleic acid extraction examples: - - value: V6, V9, ITS + - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf in_subset: - sequencing from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - target - slot_uri: MIXS:0000045 + slot_uri: MIXS:0000037 multivalued: false range: string - tax_class: - name: tax_class - description: Method used for taxonomic classification, along with reference database - used, classification rank, and thresholds used to classify new genomes - title: taxonomic classification + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + nucl_acid_ext_kit: + name: nucl_acid_ext_kit + annotations: + Expected_value: + tag: Expected_value + value: The name of an extraction kit + description: The name of the extraction kit used to recover the nucleic acid fraction + of an input material is performed + title: nucleic acid extraction kit examples: - - value: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, - default parameters) - in_subset: - - sequencing + - value: Qiagen PowerSoil Kit from_schema: https://w3id.org/mixs-6-2-rc keywords: - - classification - - taxon - slot_uri: MIXS:0000064 - multivalued: false - range: string - tax_ident: - name: tax_ident - description: The phylogenetic marker(s) used to assign an organism name to the - SAG or MAG - title: taxonomic identity marker + - kit + string_serialization: '{text}' + slot_uri: MIXS:0001223 + multivalued: true + required: false + recommended: false + num_replicons: + name: num_replicons + annotations: + Expected_value: + tag: Expected_value + value: 'for eukaryotes and bacteria: chromosomes (haploid count); for viruses: + segments' + description: Reports the number of replicons in a nuclear genome of eukaryotes, + in the genome of a bacterium or archaea or the number of segments in a segmented + virus. Always applied to the haploid chromosome count of a eukaryote + title: number of replicons examples: - - value: other - description: was other rpoB gene + - value: '2' in_subset: - - sequencing + - nucleic acid sequence source from_schema: https://w3id.org/mixs-6-2-rc keywords: - - identifier - - marker - - taxon - slot_uri: MIXS:0000053 - range: TAX_IDENT_ENUM - temp: - name: temp - annotations: - Preferred_unit: - tag: Preferred_unit - value: degree Celsius - description: Temperature of the sample at the time of sampling - title: temperature + - number + string_serialization: '{integer}' + slot_uri: MIXS:0000022 + range: integer + num_samp_collect: + name: num_samp_collect + description: The number of samples collected during the current sampling event + title: number of samples collected examples: - - value: 25 degree Celsius - in_subset: - - environment + - value: 116 samples from_schema: https://w3id.org/mixs-6-2-rc keywords: - - temperature - slot_uri: MIXS:0000113 + - number + - sample + slot_uri: MIXS:0001224 multivalued: false range: string + required: false + recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - temp_out: - name: temp_out - annotations: - Preferred_unit: - tag: Preferred_unit - value: degree Celsius - description: The recorded temperature value at sampling time outside - title: temperature outside house + number_contig: + name: number_contig + description: Total number of contigs in the cleaned/submitted assembly that makes + up a given genome, SAG, MAG, or UViG + title: number of contigs examples: - - value: 5 degree Celsius + - value: '40' + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - house - - temperature - slot_uri: MIXS:0000197 + - number + slot_uri: MIXS:0000060 + multivalued: false + range: integer + number_pets: + name: number_pets + description: The number of pets residing in the sampled space + title: number of pets + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - number + slot_uri: MIXS:0000231 multivalued: false range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: ^{integer} {text}$ interpolated: true partial_match: true - tertiary_treatment: - name: tertiary_treatment - annotations: - Expected_value: - tag: Expected_value - value: tertiary treatment type - description: The process providing a final treatment stage to raise the effluent - quality before it is discharged to the receiving environment - title: tertiary treatment + number_plants: + name: number_plants + description: The number of plant(s) in the sampling space + title: number of houseplants from_schema: https://w3id.org/mixs-6-2-rc keywords: - - treatment - string_serialization: '{text}' - slot_uri: MIXS:0000352 + - number + slot_uri: MIXS:0000230 multivalued: false + range: string required: false recommended: false - tidal_stage: - name: tidal_stage - description: Stage of tide - title: tidal stage - examples: - - value: high tide - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000750 - multivalued: false - range: TIDAL_STAGE_ENUM - required: false - recommended: false - tillage: - name: tillage - description: Note method(s) used for tilling - title: history/tillage - examples: - - value: chisel - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - history - slot_uri: MIXS:0001081 - multivalued: true - range: TILLAGE_ENUM - time_last_toothbrush: - name: time_last_toothbrush - description: Specification of the time since last toothbrushing - title: time since last toothbrushing - comments: - - P2H45M does not match ^P(?!$)(\\d+Y)?(\\d+M)?(\\d+W)?(\\d+D)?(T(?=\\d+[HMS])(\\d+H)?(\\d+M)?(\\d+S)?)?$ - - problematic ISO 8601 period validation - examples: - - value: PT2H45M - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - time - slot_uri: MIXS:0000924 - range: string - required: false - recommended: false - pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ - structured_pattern: - syntax: ^{duration}$ - interpolated: true - partial_match: true - time_since_last_wash: - name: time_since_last_wash - description: Specification of the time since last wash - title: time since last wash - examples: - - value: P1D + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + number_resident: + name: number_resident + description: The number of individuals currently occupying in the sampling location + title: number of residents from_schema: https://w3id.org/mixs-6-2-rc keywords: - - time - slot_uri: MIXS:0000943 + - number + slot_uri: MIXS:0000232 multivalued: false range: string required: false recommended: false - pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{duration}$ + syntax: ^{integer} {text}$ interpolated: true partial_match: true - timepoint: - name: timepoint - annotations: - Preferred_unit: - tag: Preferred_unit - value: hours or days - description: Time point at which a sample or observation is made or taken from - a biomaterial as measured from some reference point. Indicate the timepoint - written in ISO 8601 format - title: timepoint + occup_density_samp: + name: occup_density_samp + description: Average number of occupants at time of sampling per square footage + title: occupant density at sampling examples: - - value: PT24H + - value: '0.1' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - time - slot_uri: MIXS:0001173 + - density + slot_uri: MIXS:0000217 multivalued: false - range: string - required: false - recommended: false - pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ - structured_pattern: - syntax: ^{duration}$ - interpolated: true - partial_match: true - tiss_cult_growth_med: - name: tiss_cult_growth_med - description: Description of plant tissue culture growth media used - title: tissue culture growth media + range: float + required: true + occup_document: + name: occup_document + description: The type of documentation of occupancy + title: occupancy documentation examples: - - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf + - value: estimate from_schema: https://w3id.org/mixs-6-2-rc keywords: - - culture - - growth - slot_uri: MIXS:0001070 + - documentation + slot_uri: MIXS:0000816 multivalued: false - range: string + range: OCCUP_DOCUMENT_ENUM required: false recommended: false - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}|{text}$ - interpolated: true - partial_match: true - toluene: - name: toluene - annotations: - Preferred_unit: - tag: Preferred_unit - value: milligram per liter, parts per million - description: Concentration of toluene in the sample - title: toluene + occup_samp: + name: occup_samp + description: Number of occupants present at time of sample within the given space + title: occupancy at sampling + examples: + - value: '10' from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000154 - multivalued: false - range: string - recommended: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + slot_uri: MIXS:0000772 + range: float + required: true + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: ^{integer} {text}$ interpolated: true partial_match: true - tot_carb: - name: tot_carb - description: Total carbon content - title: total carbon + org_carb: + name: org_carb + description: Concentration of organic carbon + title: organic carbon + examples: + - value: 1.5 microgram per liter from_schema: https://w3id.org/mixs-6-2-rc keywords: - carbon - - total - slot_uri: MIXS:0000525 + - organic + slot_uri: MIXS:0000508 multivalued: false range: string + required: false + recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - tot_depth_water_col: - name: tot_depth_water_col + org_count_qpcr_info: + name: org_count_qpcr_info annotations: + Expected_value: + tag: Expected_value + value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial + denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final + elongation:degrees_minutes; total cycles Preferred_unit: tag: Preferred_unit - value: meter - description: Measurement of total depth of water column - title: total depth of water column - examples: - - value: 500 meter + value: number of cells per gram (or ml or cm^2) + description: 'If qpcr was used for the cell count, the target gene name, the primer + sequence and the cycling conditions should also be provided. (Example: 16S rrna; + FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; + annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; + 30 cycles)' + title: organism count qPCR information from_schema: https://w3id.org/mixs-6-2-rc keywords: - - depth - - total - - water - slot_uri: MIXS:0000634 + - count + - information + - organism + string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final + elongation:degrees_minutes; total cycles' + slot_uri: MIXS:0000099 multivalued: false - range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - tot_diss_nitro: - name: tot_diss_nitro + org_matter: + name: org_matter annotations: Preferred_unit: tag: Preferred_unit value: microgram per liter - description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured - by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen' - title: total dissolved nitrogen + description: Concentration of organic matter + title: organic matter examples: - - value: 40 microgram per liter + - value: 1.75 milligram per cubic meter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - dissolved - - nitrogen - - total - slot_uri: MIXS:0000744 + - organic + slot_uri: MIXS:0000204 multivalued: false range: string required: false @@ -16218,22 +13965,17 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - tot_inorg_nitro: - name: tot_inorg_nitro - annotations: - Preferred_unit: - tag: Preferred_unit - value: microgram per liter - description: Total inorganic nitrogen content - title: total inorganic nitrogen + org_nitro: + name: org_nitro + description: Concentration of organic nitrogen + title: organic nitrogen examples: - - value: 40 microgram per liter + - value: 4 micromole per liter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - inorganic - nitrogen - - total - slot_uri: MIXS:0000745 + - organic + slot_uri: MIXS:0000205 multivalued: false range: string required: false @@ -16244,156 +13986,181 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - tot_iron: - name: tot_iron + org_particles: + name: org_particles annotations: + Expected_value: + tag: Expected_value + value: particle name;measurement value Preferred_unit: tag: Preferred_unit - value: milligram per liter, milligram per kilogram - description: Concentration of total iron in the sample - title: total iron + value: gram per liter + description: Concentration of particles such as faeces, hairs, food, vomit, paper + fibers, plant material, humus, etc + title: organic particles from_schema: https://w3id.org/mixs-6-2-rc keywords: - - total - slot_uri: MIXS:0000105 - multivalued: false - range: string - recommended: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - tot_nitro: - name: tot_nitro + - organic + - particle + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000665 + multivalued: true + required: false + recommended: false + organism_count: + name: organism_count annotations: - Preferred_unit: - tag: Preferred_unit - value: microgram per liter, micromole per liter, milligram per liter - description: 'Total nitrogen concentration of water samples, calculated by: total - nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured - without filtering, reported as nitrogen' - title: total nitrogen concentration + Expected_value: + tag: Expected_value + value: organism name;measurement value;enumeration + description: 'Total cell count of any organism (or group of organisms) per gram, + volume or area of sample, should include name of organism followed by count. + The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should + also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)' + title: organism count + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - count + - organism + string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]' + slot_uri: MIXS:0000103 + multivalued: true + otu_class_appr: + name: otu_class_appr + annotations: + Expected_value: + tag: Expected_value + value: cutoffs and method used + description: Cutoffs and approach used when clustering species-level OTUs. Note + that results from standard 95% ANI / 85% AF clustering should be provided alongside + OTUS defined from another set of thresholds, even if the latter are the ones + primarily used during the analysis + title: OTU classification approach examples: - - value: 50 micromole per liter + - value: 95% ANI;85% AF; greedy incremental clustering + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - concentration - - nitrogen - - total - slot_uri: MIXS:0000102 + - classification + - otu + string_serialization: '{ANI cutoff};{AF cutoff};{clustering method}' + slot_uri: MIXS:0000085 multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - tot_nitro_cont_meth: - name: tot_nitro_cont_meth - description: Reference or method used in determining the total nitrogen - title: total nitrogen content method + otu_db: + name: otu_db + annotations: + Expected_value: + tag: Expected_value + value: database and version + description: Reference database (i.e. sequences not generated as part of the current + study) used to cluster new genomes in "species-level" OTUs, if any + title: OTU database examples: - - value: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 + - value: NCBI Viral RefSeq;83 + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - content - - method - - nitrogen - - total - slot_uri: MIXS:0000338 + - database + - otu + string_serialization: '{database};{version}' + slot_uri: MIXS:0000087 multivalued: false - range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ - structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ - interpolated: true - partial_match: true - tot_nitro_content: - name: tot_nitro_content - description: Total nitrogen content of the sample - title: total nitrogen content + otu_seq_comp_appr: + name: otu_seq_comp_appr + annotations: + Expected_value: + tag: Expected_value + value: software name, version and relevant parameters + description: Tool and thresholds used to compare sequences when computing "species-level" + OTUs + title: OTU sequence comparison approach examples: - - value: 35 milligrams Nitrogen per kilogram of soil + - value: 'blastn;2.6.0+;e-value cutoff: 0.001' + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - content - - nitrogen - - total - slot_uri: MIXS:0000530 + - otu + string_serialization: '{software};{version};{parameters}' + slot_uri: MIXS:0000086 + multivalued: false + owc_tvdss: + name: owc_tvdss + annotations: + Preferred_unit: + tag: Preferred_unit + value: meter + description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + title: oil water contact depth + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - depth + - oil + - water + slot_uri: MIXS:0000405 multivalued: false range: string + required: false + recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - tot_org_c_meth: - name: tot_org_c_meth - description: Reference or method used in determining total organic carbon - title: total organic carbon method + oxy_stat_samp: + name: oxy_stat_samp + description: Oxygenation status of sample + title: oxygenation status of sample examples: - - value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf + - value: aerobic from_schema: https://w3id.org/mixs-6-2-rc keywords: - - carbon - - method - - organic - - total - slot_uri: MIXS:0000337 + - oxygen + - sample + - status + slot_uri: MIXS:0000753 multivalued: false - range: string - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ - structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ - interpolated: true - partial_match: true - tot_org_carb: - name: tot_org_carb + range: OXY_STAT_SAMP_ENUM + oxygen: + name: oxygen annotations: Preferred_unit: tag: Preferred_unit - value: gram Carbon per kilogram sample material - description: Total organic carbon content - title: total organic carbon + value: milligram per liter, parts per million + description: Oxygen (gas) amount or concentration at the time of sampling + title: oxygen examples: - - value: '0.02' + - value: 600 parts per million from_schema: https://w3id.org/mixs-6-2-rc keywords: - - carbon - - organic - - total - slot_uri: MIXS:0000533 + - oxygen + slot_uri: MIXS:0000104 multivalued: false range: string + required: false + recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - tot_part_carb: - name: tot_part_carb - annotations: - Preferred_unit: - tag: Preferred_unit - value: microgram per liter, micromole per liter - description: Total particulate carbon content - title: total particulate carbon + part_org_carb: + name: part_org_carb + description: Concentration of particulate organic carbon + title: particulate organic carbon examples: - - value: 35 micromole per liter + - value: 1.92 micromole per liter from_schema: https://w3id.org/mixs-6-2-rc keywords: - carbon + - organic - particle - particulate - - total - slot_uri: MIXS:0000747 + slot_uri: MIXS:0000515 multivalued: false range: string required: false @@ -16404,22 +14171,23 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - tot_phosp: - name: tot_phosp + part_org_nitro: + name: part_org_nitro annotations: Preferred_unit: tag: Preferred_unit - value: micromole per liter, milligram per liter, parts per million - description: 'Total phosphorus concentration in the sample, calculated by: total - phosphorus = total dissolved phosphorus + particulate phosphorus' - title: total phosphorus + value: microgram per liter, micromole per liter + description: Concentration of particulate organic nitrogen + title: particulate organic nitrogen examples: - - value: 0.03 milligram per liter + - value: 0.3 micromole per liter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - phosphorus - - total - slot_uri: MIXS:0000117 + - nitrogen + - organic + - particle + - particulate + slot_uri: MIXS:0000719 multivalued: false range: string required: false @@ -16430,198 +14198,202 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - tot_phosphate: - name: tot_phosphate + part_plant_animal: + name: part_plant_animal annotations: - Preferred_unit: - tag: Preferred_unit - value: microgram per liter, micromole per liter - description: Total amount or concentration of phosphate - title: total phosphate + Expected_value: + tag: Expected_value + value: FOODON:03420116 + description: The anatomical part of the organism being involved in food production + or consumption; e.g., a carrot is the root of the plant (root vegetable). This + field accepts terms listed under part of plant or animal (http://purl.obolibrary.org/obo/FOODON_03420116) + title: part of plant or animal + examples: + - value: chuck [FOODON:03530021] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - phosphate - - total - slot_uri: MIXS:0000689 - multivalued: false - range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - tot_sulfur: - name: tot_sulfur + - animal + - plant + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001149 + multivalued: true + required: false + recommended: false + particle_class: + name: particle_class annotations: + Expected_value: + tag: Expected_value + value: particle name;measurement value Preferred_unit: tag: Preferred_unit - value: milligram per liter, parts per million - description: Concentration of total sulfur in the sample - title: total sulfur - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - sulfur - - total - slot_uri: MIXS:0000419 - multivalued: false - range: string - recommended: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - train_line: - name: train_line - description: The subway line name - title: train line - examples: - - value: red - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - train - slot_uri: MIXS:0000837 - multivalued: false - range: TRAIN_LINE_ENUM - required: false - recommended: false - train_stat_loc: - name: train_stat_loc - description: The train station collection location - title: train station collection location - examples: - - value: forest hills + value: micrometer + description: Particles are classified, based on their size, into six general categories:clay, + silt, sand, gravel, cobbles, and boulders; should include amount of particle + preceded by the name of the particle type; can include multiple values + title: particle classification from_schema: https://w3id.org/mixs-6-2-rc keywords: - - location - - train - slot_uri: MIXS:0000838 - multivalued: false - range: TRAIN_STAT_LOC_ENUM + - classification + - particle + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000206 + multivalued: true required: false recommended: false - train_stop_loc: - name: train_stop_loc - description: The train stop collection location - title: train stop collection location + pathogenicity: + name: pathogenicity + annotations: + Expected_value: + tag: Expected_value + value: names of organisms that the entity is pathogenic to + description: To what is the entity pathogenic + title: known pathogenicity examples: - - value: end + - value: human, animal, plant, fungi, bacteria + in_subset: + - nucleic acid sequence source from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - location - - stop - - train - slot_uri: MIXS:0000839 + string_serialization: '{text}' + slot_uri: MIXS:0000027 multivalued: false - range: TRAIN_STOP_LOC_ENUM - required: false - recommended: false - travel_out_six_month: - name: travel_out_six_month + pcr_cond: + name: pcr_cond annotations: Expected_value: tag: Expected_value - value: country name - description: Specification of the countries travelled in the last six months; - can include multiple travels - title: travel outside the country in last six months - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - months - string_serialization: '{text}' - slot_uri: MIXS:0000268 - multivalued: true - required: false - recommended: false - trna_ext_software: - name: trna_ext_software - description: Tools used for tRNA identification - title: tRNA extraction software + value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final + elongation:degrees_minutes;total cycles + description: Description of reaction conditions and components of PCR in the form + of 'initial denaturation:94degC_1.5min; annealing=...' + title: pcr conditions examples: - - value: infernal;v2;default parameters + - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 in_subset: - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - software - slot_uri: MIXS:0000068 + - condition + - pcr + string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final + elongation:degrees_minutes;total cycles + slot_uri: MIXS:0000049 multivalued: false - range: string - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{software};{version};{parameters}$ - interpolated: true - partial_match: true - trnas: - name: trnas + pcr_primers: + name: pcr_primers annotations: Expected_value: tag: Expected_value - value: value from 0-21 - description: The total number of tRNAs identified from the SAG or MAG - title: number of standard tRNAs extracted + value: 'FWD: forward primer sequence;REV:reverse primer sequence' + description: PCR primers that were used to amplify the sequence of the targeted + gene, locus or subfragment. This field should contain all the primers used for + a single PCR reaction if multiple forward or reverse primers are present in + a single PCR reaction. The primer sequence should be reported in uppercase letters + title: pcr primers examples: - - value: '18' + - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT in_subset: - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - number - string_serialization: '{integer}' - slot_uri: MIXS:0000067 + - pcr + string_serialization: FWD:{dna};REV:{dna} + slot_uri: MIXS:0000046 multivalued: false - trophic_level: - name: trophic_level - description: Trophic levels are the feeding position in a food chain. Microbes - can be a range of producers (e.g. chemolithotroph) - title: trophic level + permeability: + name: permeability + annotations: + Expected_value: + tag: Expected_value + value: measurement value range + Preferred_unit: + tag: Preferred_unit + value: mD + description: 'Measure of the ability of a hydrocarbon resource to allow fluids + to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))' + title: permeability + from_schema: https://w3id.org/mixs-6-2-rc + string_serialization: '{integer} - {integer} {unit}' + slot_uri: MIXS:0000404 + multivalued: false + required: false + recommended: false + perturbation: + name: perturbation + annotations: + Expected_value: + tag: Expected_value + value: perturbation type name;perturbation interval and duration + description: Type of perturbation, e.g. chemical administration, physical disturbance, + etc., coupled with perturbation regimen including how many times the perturbation + was repeated, how long each perturbation lasted, and the start and end time + of the entire perturbation period; can include multiple perturbation types + title: perturbation examples: - - value: heterotroph - in_subset: - - nucleic acid sequence source + - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M from_schema: https://w3id.org/mixs-6-2-rc keywords: - - level - slot_uri: MIXS:0000032 - multivalued: false - range: TROPHIC_LEVEL_ENUM - turbidity: - name: turbidity - description: Measure of the amount of cloudiness or haziness in water caused by - individual particles - title: turbidity + - perturbation + string_serialization: '{text};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000754 + multivalued: true + pesticide_regm: + name: pesticide_regm + annotations: + Preferred_unit: + tag: Preferred_unit + value: gram, mole per liter, milligram per liter + description: Information about treatment involving use of insecticides; should + include the name of pesticide, amount administered, treatment regimen including + how many times the treatment was repeated, how long each treatment lasted, and + the start and end time of the entire treatment; can include multiple pesticide + regimens + title: pesticide regimen examples: - - value: 0.3 nephelometric turbidity units + - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000191 - multivalued: false + keywords: + - regimen + slot_uri: MIXS:0000573 + multivalued: true range: string + pet_farm_animal: + name: pet_farm_animal + annotations: + Expected_value: + tag: Expected_value + value: presence status;type of animal or pet + description: Specification of presence of pets or farm animals in the environment + of subject, if yes the animals should be specified; can include multiple animals + present + title: presence of pets or farm animals + examples: + - value: yes; 5 cats + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - animal + - farm + - presence + string_serialization: '{boolean};{text}' + slot_uri: MIXS:0000267 + multivalued: true required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - tvdss_of_hcr_press: - name: tvdss_of_hcr_press + petroleum_hydrocarb: + name: petroleum_hydrocarb annotations: Preferred_unit: tag: Preferred_unit - value: meter - description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where - the original pressure was measured (e.g. 1578 m) - title: depth (TVDSS) of hydrocarbon resource pressure + value: micromole per liter + description: Concentration of petroleum hydrocarbon + title: petroleum hydrocarbon + examples: + - value: 0.05 micromole per liter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - depth - hydrocarbon - - pressure - - resource - slot_uri: MIXS:0000397 + - petroleum + slot_uri: MIXS:0000516 multivalued: false range: string required: false @@ -16632,148 +14404,86 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - tvdss_of_hcr_temp: - name: tvdss_of_hcr_temp - annotations: - Preferred_unit: - tag: Preferred_unit - value: meter - description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where - the original temperature was measured (e.g. 1345 m) - title: depth (TVDSS) of hydrocarbon resource temperature - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - depth - - hydrocarbon - - resource - - temperature - slot_uri: MIXS:0000394 - multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - twin_sibling: - name: twin_sibling - description: Specification of twin sibling presence - title: twin sibling presence - examples: - - value: 'yes' - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - presence - slot_uri: MIXS:0000326 - multivalued: false - range: boolean - required: false - recommended: false - typ_occup_density: - name: typ_occup_density - description: Customary or normal density of occupants - title: typical occupant density + ph: + name: ph + description: Ph measurement of the sample, or liquid portion of sample, or aqueous + phase of the fluid + title: pH examples: - - value: '25' + - value: '7.2' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - density - slot_uri: MIXS:0000771 + - ph + slot_uri: MIXS:0001001 multivalued: false range: float - required: true - type_of_symbiosis: - name: type_of_symbiosis - description: Type of biological interaction established between the symbiotic - host organism being sampled and its respective host - title: type of symbiosis + ph_meth: + name: ph_meth + description: Reference or method used in determining pH + title: pH method examples: - - value: parasitic + - value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf from_schema: https://w3id.org/mixs-6-2-rc keywords: - - symbiosis - - type - slot_uri: MIXS:0001307 + - method + - ph + slot_uri: MIXS:0001106 multivalued: false - range: TYPE_OF_SYMBIOSIS_ENUM - recommended: true - urine_collect_meth: - name: urine_collect_meth - description: Specification of urine collection method - title: urine/collection method + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + ph_regm: + name: ph_regm + description: Information about treatment involving exposure of plants to varying + levels of ph of the growth media, treatment regimen including how many times + the treatment was repeated, how long each treatment lasted, and the start and + end time of the entire treatment; can include multiple regimen + title: pH regimen examples: - - value: catheter + - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc keywords: - - method - slot_uri: MIXS:0000899 - multivalued: false - range: URINE_COLLECT_METH_ENUM - required: false - recommended: false - urobiom_sex: - name: urobiom_sex + - ph + - regimen + slot_uri: MIXS:0001056 + multivalued: true + range: string + phaeopigments: + name: phaeopigments annotations: Expected_value: tag: Expected_value - value: sex of the symbiotic organism (host of the samples); enumeration - description: Physical sex of the host - title: host sex - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - host - - host. - slot_uri: MIXS:0000862 - multivalued: false - range: UROBIOM_SEX_ENUM - required: false - recommended: false - urogenit_disord: - name: urogenit_disord - description: History of urogenital disorders, can include multiple disorders. - The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary - system disease (https://disease-ontology.org/?id=DOID:18) - title: urogenital disorder - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - disorder - slot_uri: MIXS:0000289 - multivalued: true - range: string - required: false - recommended: false - urogenit_tract_disor: - name: urogenit_tract_disor - description: History of urogenital tract disorders; can include multiple disorders. - The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, - urinary system disease (https://disease-ontology.org/?id=DOID:18) - title: urine/urogenital tract disorder + value: phaeopigment name;measurement value + Preferred_unit: + tag: Preferred_unit + value: milligram per cubic meter + description: Concentration of phaeopigments; can include multiple phaeopigments + title: phaeopigments + examples: + - value: 2.5 milligram per cubic meter from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - disorder - slot_uri: MIXS:0000278 + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000180 multivalued: true - range: string required: false recommended: false - ventilation_rate: - name: ventilation_rate + phosphate: + name: phosphate annotations: Preferred_unit: tag: Preferred_unit - value: cubic meter per minute, liters per second - description: Ventilation rate of the system in the sampled premises - title: ventilation rate + value: micromole per liter + description: Concentration of phosphate + title: phosphate examples: - - value: 750 cubic meter per minute + - value: 0.7 micromole per liter from_schema: https://w3id.org/mixs-6-2-rc keywords: - - rate - slot_uri: MIXS:0000114 + - phosphate + slot_uri: MIXS:0000505 multivalued: false range: string required: false @@ -16784,370 +14494,326 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - ventilation_type: - name: ventilation_type + phosplipid_fatt_acid: + name: phosplipid_fatt_acid annotations: Expected_value: tag: Expected_value - value: ventilation type name - description: Ventilation system used in the sampled premises - title: ventilation type + value: phospholipid fatty acid name;measurement value + description: Concentration of phospholipid fatty acids; can include multiple values + title: phospholipid fatty acid examples: - - value: Operable windows + - value: 2.98 milligram per liter from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - type - string_serialization: '{text}' - slot_uri: MIXS:0000756 + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000181 multivalued: true - vfa: - name: vfa + required: false + recommended: false + photon_flux: + name: photon_flux annotations: Preferred_unit: tag: Preferred_unit - value: milligram per liter, parts per million - description: Concentration of Volatile Fatty Acids in the sample - title: volatile fatty acids + value: number of photons per second per unit area + description: Measurement of photon flux + title: photon flux + examples: + - value: 3.926 micromole photons per second per square meter from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000152 + slot_uri: MIXS:0000725 multivalued: false range: string - recommended: true + required: false + recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - vfa_fw: - name: vfa_fw + photosynt_activ: + name: photosynt_activ annotations: Preferred_unit: tag: Preferred_unit - value: milligram per liter - description: Original volatile fatty acid concentration in the hydrocarbon resource - title: vfa in formation water + value: mol m-2 s-1 + description: Measurement of photosythetic activity (i.e. leaf gas exchange / chlorophyll + fluorescence emissions / reflectance / transpiration) Please also include the + term method term detailing the method of activity measurement + title: photosynthetic activity + examples: + - value: 0.1 mol CO2 m-2 s-1 + description: added a magnitude to the example from the XLSX file, " mol CO2 + m-2 s-1" from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - water - slot_uri: MIXS:0000408 - multivalued: false + slot_uri: MIXS:0001296 range: string + recommended: true pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - vir_ident_software: - name: vir_ident_software + photosynt_activ_meth: + name: photosynt_activ_meth + description: Reference or method used in measurement of photosythetic activity + title: photosynthetic activity method + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - method + slot_uri: MIXS:0001336 + multivalued: true + range: string + recommended: true + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}|{text}$ + interpolated: true + partial_match: true + plant_growth_med: + name: plant_growth_med annotations: Expected_value: tag: Expected_value - value: software name, version and relevant parameters - description: Tool(s) used for the identification of UViG as a viral genome, software - or protocol name including version number, parameters, and cutoffs used - title: viral identification software - examples: - - value: VirSorter; 1.0.4; Virome database, category 2 - in_subset: - - sequencing - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - identifier - - software - string_serialization: '{software};{version};{parameters}' - slot_uri: MIXS:0000081 - multivalued: false - virus_enrich_appr: - name: virus_enrich_appr - description: List of approaches used to enrich the sample for viruses, if any - title: virus enrichment approach - examples: - - value: filtration - description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse - - value: FeCl Precipitation - description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse - - value: ultracentrifugation - description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse - - value: DNAse - description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse - in_subset: - - nucleic acid sequence source + value: EO or enumeration + description: Specification of the media for growing the plants or tissue cultured + samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in + vitro liquid culture medium. Recommended value is a specific value from EO:plant + growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) + or other controlled vocabulary + title: plant growth medium from_schema: https://w3id.org/mixs-6-2-rc keywords: - - enrichment - slot_uri: MIXS:0000036 - range: VIRUS_ENRICH_APPR_ENUM - vis_media: - name: vis_media - annotations: - Expected_value: - tag: Expected_value - value: enumeration - description: The building visual media - title: visual media - examples: - - value: 3D scans - from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '[photos|videos|commonly of the building|site context (adjacent - buildings, vegetation, terrain, streets)|interiors|equipment|3D scans]' - slot_uri: MIXS:0000840 + - growth + - plant + string_serialization: '{termLabel} [{termID}] or [husk|other artificial liquid + medium|other artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water]' + slot_uri: MIXS:0001057 multivalued: false required: false recommended: false - viscosity: - name: viscosity + plant_part_maturity: + name: plant_part_maturity annotations: Expected_value: tag: Expected_value - value: measurement value;measurement value - Preferred_unit: - tag: Preferred_unit - value: cP at degree Celsius - description: A measure of oil's resistance to gradual deformation by shear stress or tensile - stress (e.g. 3.5 cp; 100 C) - title: viscosity + value: FOODON:03530050 + description: A description of the stage of development of a plant or plant part + based on maturity or ripeness. This field accepts terms listed under degree + of plant maturity (http://purl.obolibrary.org/obo/FOODON_03530050) + title: degree of plant part maturity + examples: + - value: ripe or mature [FOODON:03530052] from_schema: https://w3id.org/mixs-6-2-rc - string_serialization: '{float} {unit};{float} {unit}' - slot_uri: MIXS:0000126 + keywords: + - degree + - plant + string_serialization: '{term label}{term ID}' + slot_uri: MIXS:0001120 multivalued: false required: false recommended: false - volatile_org_comp: - name: volatile_org_comp + plant_product: + name: plant_product annotations: Expected_value: tag: Expected_value - value: volatile organic compound name;measurement value - Preferred_unit: - tag: Preferred_unit - value: microgram per cubic meter, parts per million, nanogram per liter - description: Concentration of carbon-based chemicals that easily evaporate at - room temperature; can report multiple volatile organic compounds by entering - numeric values preceded by name of compound - title: volatile organic compounds + value: product name + description: Substance produced by the plant, where the sample was obtained from + title: plant product examples: - - value: formaldehyde;500 nanogram per liter - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - organic - string_serialization: '{text};{float} {unit}' - slot_uri: MIXS:0000115 - multivalued: true - required: false - recommended: false - wall_area: - name: wall_area - annotations: - Preferred_unit: - tag: Preferred_unit - value: square meter - description: The total area of the sampled room's walls - title: wall area + - value: xylem sap [PO:0025539] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - area - - wall - slot_uri: MIXS:0000198 + - plant + - product + string_serialization: '{text}' + slot_uri: MIXS:0001058 multivalued: false - range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - wall_const_type: - name: wall_const_type - description: The building class of the wall defined by the composition of the - building elements and fire-resistance rating - title: wall construction type + plant_reprod_crop: + name: plant_reprod_crop + description: Plant reproductive part used in the field during planting to start + the crop + title: plant reproductive part examples: - - value: fire resistive + - value: seedling from_schema: https://w3id.org/mixs-6-2-rc keywords: - - type - - wall - slot_uri: MIXS:0000841 - multivalued: false - range: WALL_CONST_TYPE_ENUM + - plant + slot_uri: MIXS:0001150 + multivalued: true + range: PLANT_REPROD_CROP_ENUM required: false recommended: false - wall_finish_mat: - name: wall_finish_mat - description: The material utilized to finish the outer most layer of the wall - title: wall finish material + plant_sex: + name: plant_sex + description: Sex of the reproductive parts on the whole plant, e.g. pistillate, + staminate, monoecieous, hermaphrodite + title: plant sex examples: - - value: wood + - value: Hermaphroditic from_schema: https://w3id.org/mixs-6-2-rc keywords: - - material - - wall - slot_uri: MIXS:0000842 + - plant + slot_uri: MIXS:0001059 multivalued: false - range: WALL_FINISH_MAT_ENUM + range: PLANT_SEX_ENUM required: false recommended: false - wall_height: - name: wall_height - annotations: - Preferred_unit: - tag: Preferred_unit - value: centimeter - description: The average height of the walls in the sampled room - title: wall height + plant_struc: + name: plant_struc + description: Name of plant structure the sample was obtained from; for Plant Ontology + (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, + e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the + sex of it can be recorded here + title: plant structure + examples: + - value: epidermis [PO:0005679] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - height - - wall - slot_uri: MIXS:0000221 + - plant + slot_uri: MIXS:0001060 multivalued: false range: string - required: false - recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + syntax: ^{termLabel} \[{termID}\]$ interpolated: true partial_match: true - wall_loc: - name: wall_loc - description: The relative location of the wall within the room - title: wall location + plant_water_method: + name: plant_water_method + description: Description of the equipment or method used to distribute water to + crops. This field accepts termed listed under irrigation process (http://purl.obolibrary.org/obo/AGRO_00000006). + Multiple terms can be separated by pipes + title: plant water delivery method examples: - - value: north + - value: drip irrigation process [AGRO:00000056] from_schema: https://w3id.org/mixs-6-2-rc keywords: - - location - - wall - slot_uri: MIXS:0000843 + - delivery + - method + - plant + - water + slot_uri: MIXS:0001111 multivalued: false - range: SHARED_ENUM_0 - required: false - recommended: false - wall_surf_treatment: - name: wall_surf_treatment - description: The surface treatment of interior wall - title: wall surface treatment + range: string + recommended: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + ploidy: + name: ploidy + description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, + triploid, tetraploid). It has implications for the downstream study of duplicated + gene and regions of the genomes (and perhaps for difficulties in assembly). + For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic + Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer + to http://purl.bioontology.org/ontology/PATO + title: ploidy examples: - - value: paneling + - value: allopolyploidy [PATO:0001379] + in_subset: + - nucleic acid sequence source from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - surface - - treatment - - wall - slot_uri: MIXS:0000845 + slot_uri: MIXS:0000021 multivalued: false - range: WALL_SURF_TREATMENT_ENUM - required: false - recommended: false - wall_texture: - name: wall_texture - description: The feel, appearance, or consistency of a wall surface - title: wall texture - examples: - - value: popcorn - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - texture - - wall - slot_uri: MIXS:0000846 - multivalued: false - range: SHARED_ENUM_4 - required: false - recommended: false - wall_thermal_mass: - name: wall_thermal_mass + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + pollutants: + name: pollutants annotations: + Expected_value: + tag: Expected_value + value: pollutant name;measurement value Preferred_unit: tag: Preferred_unit - value: joule per degree Celsius - description: The ability of the wall to provide inertia against temperature fluctuations. - Generally this means concrete or concrete block that is either exposed or covered - only with paint - title: wall thermal mass + value: gram, mole per liter, milligram per liter, microgram per cubic meter + description: Pollutant types and, amount or concentrations measured at the time + of sampling; can report multiple pollutants by entering numeric values preceded + by name of pollutant + title: pollutants + examples: + - value: lead;0.15 microgram per cubic meter from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - mass - - wall - slot_uri: MIXS:0000222 - multivalued: false - range: string + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000107 + multivalued: true required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - wall_water_mold: - name: wall_water_mold - description: Signs of the presence of mold or mildew on a wall - title: wall signs of water/mold + pool_dna_extracts: + name: pool_dna_extracts + annotations: + Expected_value: + tag: Expected_value + value: pooling status;number of pooled extracts + Preferred_unit: + tag: Preferred_unit + value: gram, milliliter, microliter + description: Indicate whether multiple DNA extractions were mixed. If the answer + yes, the number of extracts that were pooled should be given + title: pooling of DNA extracts (if done) examples: - - value: no presence of mold visible + - value: yes, 5 from_schema: https://w3id.org/mixs-6-2-rc keywords: - - wall - slot_uri: MIXS:0000844 + - dna + - pooling + slot_uri: MIXS:0000325 multivalued: false - range: SHARED_ENUM_1 - required: false - recommended: false - wastewater_type: - name: wastewater_type + porosity: + name: porosity annotations: Expected_value: tag: Expected_value - value: wastewater type name - description: The origin of wastewater such as human waste, rainfall, storm drains, - etc - title: wastewater type + value: measurement value or range + Preferred_unit: + tag: Preferred_unit + value: percentage + description: Porosity of deposited sediment is volume of voids divided by the + total volume of sample + title: porosity from_schema: https://w3id.org/mixs-6-2-rc keywords: - - type - string_serialization: '{text}' - slot_uri: MIXS:0000353 + - porosity + string_serialization: '{float} - {float} {unit}' + slot_uri: MIXS:0000211 multivalued: false required: false recommended: false - water_cont_soil_meth: - name: water_cont_soil_meth - description: Reference or method used in determining the water content of soil - title: water content method + pos_cont_type: + name: pos_cont_type + description: The substance, mixture, product, or apparatus used to verify that + a process which is part of an investigation delivers a true positive + title: positive control type + in_subset: + - investigation from_schema: https://w3id.org/mixs-6-2-rc keywords: - - content - - method - - water - slot_uri: MIXS:0000323 + - type + string_serialization: '{term} or {text}' + slot_uri: MIXS:0001322 multivalued: false - range: string - required: false - recommended: false - pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ - structured_pattern: - syntax: ^{PMID}|{DOI}|{URL}$ - interpolated: true - partial_match: true - water_content: - name: water_content + recommended: true + potassium: + name: potassium annotations: Preferred_unit: tag: Preferred_unit - value: gram per gram or cubic centimeter per cubic centimeter - description: Water content measurement - title: water content + value: milligram per liter, parts per million + description: Concentration of potassium in the sample + title: potassium + examples: + - value: 463 milligram per liter from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - content - - water - slot_uri: MIXS:0000185 + slot_uri: MIXS:0000430 multivalued: false range: string required: false @@ -17158,20 +14824,19 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - water_current: - name: water_current + pour_point: + name: pour_point annotations: Preferred_unit: tag: Preferred_unit - value: cubic meter per second, knots - description: Measurement of magnitude and direction of flow within a fluid - title: water current - examples: - - value: 10 cubic meter per second + value: degree Celsius + description: 'Temperature at which a liquid becomes semi solid and loses its flow + characteristics. In crude oil a high pour point is generally associated with + a high paraffin content, typically found in crude deriving from a larger proportion + of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)' + title: pour point from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - water - slot_uri: MIXS:0000203 + slot_uri: MIXS:0000127 multivalued: false range: string required: false @@ -17182,2964 +14847,8119 @@ slots: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - water_cut: - name: water_cut - annotations: - Preferred_unit: - tag: Preferred_unit - value: percent - description: Current amount of water (%) in a produced fluid stream; or the average - of the combined streams - title: water cut - comments: - - percent or float? - examples: - - value: 45% - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - water - slot_uri: MIXS:0000454 - range: string - required: true - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - water_feat_size: - name: water_feat_size + pre_treatment: + name: pre_treatment annotations: - Preferred_unit: - tag: Preferred_unit - value: square meter - description: The size of the water feature - title: water feature size + Expected_value: + tag: Expected_value + value: pre-treatment type + description: The process of pre-treatment removes materials that can be easily + collected from the raw wastewater + title: pre-treatment from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - feature - - size - - water - slot_uri: MIXS:0000223 + string_serialization: '{text}' + slot_uri: MIXS:0000348 multivalued: false - range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - water_feat_type: - name: water_feat_type - description: The type of water feature present within the building being sampled - title: water feature type + pred_genome_struc: + name: pred_genome_struc + description: Expected structure of the viral genome + title: predicted genome structure examples: - - value: stream + - value: non-segmented + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - feature - - type - - water - slot_uri: MIXS:0000847 + - predict + slot_uri: MIXS:0000083 multivalued: false - range: WATER_FEAT_TYPE_ENUM - required: false - recommended: false - water_frequency: - name: water_frequency + range: PRED_GENOME_STRUC_ENUM + pred_genome_type: + name: pred_genome_type annotations: Expected_value: tag: Expected_value - value: rate - Preferred_unit: - tag: Preferred_unit - value: per day, per week, per month - description: Number of water delivery events within a given period of time - title: water delivery frequency + value: enumeration + description: Type of genome predicted for the UViG + title: predicted genome type examples: - - value: 2 per day + - value: dsDNA + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - delivery - - frequency - - water - string_serialization: '{float}{unit}' - slot_uri: MIXS:0001174 - multivalued: false + - predict + - type + string_serialization: '[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (-)|mixed|uncharacterized]' + slot_uri: MIXS:0000082 + multivalued: false + pregnancy: + name: pregnancy + description: Date due of pregnancy + title: pregnancy + examples: + - value: '2013-03-25T12:42:31+01:00' + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000966 + multivalued: false + range: datetime required: false recommended: false - water_pH: - name: water_pH - title: water pH + pres_animal_insect: + name: pres_animal_insect + annotations: + Expected_value: + tag: Expected_value + value: enumeration;count + description: The type and number of animals or insects present in the sampling + space + title: presence of pets, animals, or insects examples: - - value: '7.2' + - value: cat;5 from_schema: https://w3id.org/mixs-6-2-rc keywords: - - ph - - water - slot_uri: MIXS:0001175 + - animal + - presence + string_serialization: '[cat|dog|rodent|snake|other];{integer}' + slot_uri: MIXS:0000819 multivalued: false - range: float required: false recommended: false - water_prod_rate: - name: water_prod_rate + pressure: + name: pressure annotations: Preferred_unit: tag: Preferred_unit - value: cubic meter per day - description: Water production rates per well (e.g. 987 m3 / day) - title: water production rate + value: atmosphere + description: Pressure to which the sample is subject to, in atmospheres + title: pressure + examples: + - value: 50 atmosphere from_schema: https://w3id.org/mixs-6-2-rc keywords: - - production - - rate - - water - slot_uri: MIXS:0000453 + - pressure + slot_uri: MIXS:0000412 multivalued: false range: string - recommended: true + required: false + recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true - water_source_adjac: - name: water_source_adjac - annotations: - Expected_value: - tag: Expected_value - value: ENVO_01001110 or ENVO_00000070 - description: Description of the environmental features that are adjacent to the - farm water source. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) - and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple - terms can be separated by pipes - title: environmental feature adjacent water source - examples: - - value: feedlot [ENVO:01000627] + prev_land_use_meth: + name: prev_land_use_meth + description: Reference or method used in determining previous land use and dates + title: history/previous land use method from_schema: https://w3id.org/mixs-6-2-rc keywords: - - adjacent - - environmental - - feature - - source - - water - string_serialization: '{text}' - slot_uri: MIXS:0001122 - multivalued: true - required: false - recommended: false - water_source_shared: - name: water_source_shared + - history + - land + - method + - use + slot_uri: MIXS:0000316 + multivalued: false + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + previous_land_use: + name: previous_land_use annotations: Expected_value: tag: Expected_value - value: enumeration - description: Other users sharing access to the same water source. Multiple terms - can be separated by one or more pipes - title: water source shared + value: land use name;date + description: Previous land use and dates + title: history/previous land use examples: - - value: no sharing + - value: fallow; 2018-05-11:T14:30Z from_schema: https://w3id.org/mixs-6-2-rc keywords: - - source - - water - string_serialization: '[multiple users, agricutural|multiple users, other|no sharing]' - slot_uri: MIXS:0001176 - multivalued: true - required: false - recommended: false - water_temp_regm: - name: water_temp_regm + - history + - land + - use + string_serialization: '{text};{timestamp}' + slot_uri: MIXS:0000315 + multivalued: false + primary_prod: + name: primary_prod annotations: Preferred_unit: tag: Preferred_unit - value: degree Celsius - description: Information about treatment involving an exposure to water with varying - degree of temperature, treatment regimen including how many times the treatment - was repeated, how long each treatment lasted, and the start and end time of - the entire treatment; can include multiple regimens - title: water temperature regimen + value: milligram per cubic meter per day, gram per square meter per day + description: Measurement of primary production, generally measured as isotope + uptake + title: primary production examples: - - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: 100 milligram per cubic meter per day from_schema: https://w3id.org/mixs-6-2-rc keywords: - - regimen - - temperature - - water - slot_uri: MIXS:0000590 - multivalued: true + - primary + - production + slot_uri: MIXS:0000728 + multivalued: false range: string - watering_regm: - name: watering_regm + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + primary_treatment: + name: primary_treatment annotations: - Preferred_unit: - tag: Preferred_unit - value: milliliter, liter - description: Information about treatment involving an exposure to watering frequencies, - treatment regimen including how many times the treatment was repeated, how long - each treatment lasted, and the start and end time of the entire treatment; can - include multiple regimens - title: watering regimen + Expected_value: + tag: Expected_value + value: primary treatment type + description: The process to produce both a generally homogeneous liquid capable + of being treated biologically and a sludge that can be separately treated or + processed + title: primary treatment + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - primary + - treatment + string_serialization: '{text}' + slot_uri: MIXS:0000349 + multivalued: false + required: false + recommended: false + prod_label_claims: + name: prod_label_claims + description: Labeling claims containing descriptors such as wild caught, free-range, + organic, free-range, industrial, hormone-free, antibiotic free, cage free. Can + include more than one term, separated by ";" + title: production labeling claims examples: - - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: free range from_schema: https://w3id.org/mixs-6-2-rc keywords: - - regimen - - water - slot_uri: MIXS:0000591 + - production + slot_uri: MIXS:prod_label_claims multivalued: true range: string - weekday: - name: weekday - description: The day of the week when sampling occurred - title: weekday - examples: - - value: Sunday - from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000848 - multivalued: false - range: WEEKDAY_ENUM required: false recommended: false - weight_loss_3_month: - name: weight_loss_3_month + prod_rate: + name: prod_rate annotations: - Expected_value: - tag: Expected_value - value: weight loss specification;measurement value Preferred_unit: tag: Preferred_unit - value: kilogram, gram - description: Specification of weight loss in the last three months, if yes should - be further specified to include amount of weight loss - title: weight loss in last three months - examples: - - value: yes;5 kilogram + value: cubic meter per day + description: Oil and/or gas production rates per well (e.g. 524 m3 / day) + title: production rate from_schema: https://w3id.org/mixs-6-2-rc keywords: - - months - - weight - string_serialization: '{boolean};{float} {unit}' - slot_uri: MIXS:0000295 + - production + - rate + slot_uri: MIXS:0000452 multivalued: false - required: false - recommended: false - wga_amp_appr: - name: wga_amp_appr - description: Method used to amplify genomic DNA in preparation for sequencing - title: WGA amplification approach + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + prod_start_date: + name: prod_start_date + description: Date of field's first production + title: production start date examples: - - value: mda based - in_subset: - - sequencing + - value: '2013-03-25T12:42:31+01:00' from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000055 - multivalued: false - range: WGA_AMP_APPR_ENUM - wga_amp_kit: - name: wga_amp_kit - annotations: - Expected_value: - tag: Expected_value - value: kit name - description: Kit used to amplify genomic DNA in preparation for sequencing - title: WGA amplification kit + keywords: + - date + - production + - start + slot_uri: MIXS:0001008 + multivalued: false + range: datetime + recommended: true + profile_position: + name: profile_position + description: Cross-sectional position in the hillslope where sample was collected.sample + area position in relation to surrounding areas + title: profile position examples: - - value: qiagen repli-g - in_subset: - - sequencing + - value: summit from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - kit - string_serialization: '{text}' - slot_uri: MIXS:0000006 + slot_uri: MIXS:0001084 multivalued: false - win: - name: win - description: 'A unique identifier of a well or wellbore. This is part of the Global - Framework for Well Identification initiative which is compiled by the Professional - Petroleum Data Management Association (PPDM) in an effort to improve well identification - systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)' - title: well identification number + range: PROFILE_POSITION_ENUM + project_name: + name: project_name + description: Name of the project within which the sequencing was organized + title: project name + examples: + - value: Forest soil metagenome + in_subset: + - investigation from_schema: https://w3id.org/mixs-6-2-rc keywords: - - identifier - - number - slot_uri: MIXS:0000297 + - project + slot_uri: MIXS:0000092 multivalued: false range: string - recommended: true - wind_direction: - name: wind_direction + required: true + propagation: + name: propagation annotations: - Preferred_unit: - tag: Preferred_unit - value: degrees or cardinal direction - description: Wind direction is the direction from which a wind originates - title: wind direction + Expected_value: + tag: Expected_value + value: 'for virus: lytic, lysogenic, temperate, obligately lytic; for plasmid: + incompatibility group; for eukaryote: asexual, sexual; other more specific + values (e.g., incompatibility group) are allowed' + description: 'The type of reproduction from the parent stock. Values for this + field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately + lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual' + title: propagation + examples: + - value: lytic + in_subset: + - nucleic acid sequence source from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - direction - - wind - slot_uri: MIXS:0000757 + string_serialization: '{text}' + slot_uri: MIXS:0000033 multivalued: false - range: string - required: false - recommended: false - wind_speed: - name: wind_speed - description: speed of wind measured at the time of sampling - title: wind speed + pulmonary_disord: + name: pulmonary_disord + description: History of pulmonary disorders; can include multiple disorders. The + terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + lung disease (https://disease-ontology.org/?id=DOID:850) + title: lung/pulmonary disorder from_schema: https://w3id.org/mixs-6-2-rc keywords: - - speed - - wind - slot_uri: MIXS:0000118 - multivalued: false + - disorder + slot_uri: MIXS:0000269 + multivalued: true range: string required: false recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? - *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ - structured_pattern: - syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ - interpolated: true - partial_match: true - window_cond: - name: window_cond - description: The physical condition of the window at the time of sampling - title: window condition + quad_pos: + name: quad_pos + description: The quadrant position of the sampling room within the building + title: quadrant position examples: - - value: rupture + - value: West side from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - condition - - window - slot_uri: MIXS:0000849 + slot_uri: MIXS:0000820 multivalued: false - range: SHARED_ENUM_2 + range: QUAD_POS_ENUM required: false recommended: false - window_cover: - name: window_cover - description: The type of window covering - title: window covering + radiation_regm: + name: radiation_regm + annotations: + Expected_value: + tag: Expected_value + value: radiation type name;radiation amount;treatment interval and duration + Preferred_unit: + tag: Preferred_unit + value: rad, gray + description: Information about treatment involving exposure of plant or a plant + part to a particular radiation regimen; should include the radiation type, amount + or intensity administered, treatment regimen including how many times the treatment + was repeated, how long each treatment lasted, and the start and end time of + the entire treatment; can include multiple radiation regimens + title: radiation regimen examples: - - value: curtains + - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc keywords: - - window - slot_uri: MIXS:0000850 - multivalued: false - range: WINDOW_COVER_ENUM + - regimen + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000575 + multivalued: true required: false recommended: false - window_horiz_pos: - name: window_horiz_pos - description: The horizontal position of the window on the wall - title: window horizontal position + rainfall_regm: + name: rainfall_regm + annotations: + Expected_value: + tag: Expected_value + value: measurement value;treatment interval and duration + Preferred_unit: + tag: Preferred_unit + value: millimeter + description: Information about treatment involving an exposure to a given amount + of rainfall, treatment regimen including how many times the treatment was repeated, + how long each treatment lasted, and the start and end time of the entire treatment; + can include multiple regimens + title: rainfall regimen examples: - - value: middle + - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/mixs-6-2-rc keywords: - - window - slot_uri: MIXS:0000851 - multivalued: false - range: WINDOW_HORIZ_POS_ENUM + - rain + - regimen + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' + slot_uri: MIXS:0000576 + multivalued: true required: false recommended: false - window_loc: - name: window_loc - description: The relative location of the window within the room - title: window location - examples: - - value: west + reactor_type: + name: reactor_type + annotations: + Expected_value: + tag: Expected_value + value: reactor type name + description: Anaerobic digesters can be designed and engineered to operate using + a number of different process configurations, as batch or continuous, mesophilic, + high solid or low solid, and single stage or multistage + title: reactor type from_schema: https://w3id.org/mixs-6-2-rc keywords: - - location - - window - slot_uri: MIXS:0000852 + - type + string_serialization: '{text}' + slot_uri: MIXS:0000350 multivalued: false - range: SHARED_ENUM_0 required: false recommended: false - window_mat: - name: window_mat - description: The type of material used to finish a window - title: window material + reassembly_bin: + name: reassembly_bin + description: Has an assembly been performed on a genome bin extracted from a metagenomic + assembly? + title: reassembly post binning examples: - - value: wood - from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - material - - window - slot_uri: MIXS:0000853 - multivalued: false - range: WINDOW_MAT_ENUM - required: false - recommended: false - window_open_freq: - name: window_open_freq - description: The number of times windows are opened per week - title: window open frequency + - value: 'no' + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - frequency - - window - slot_uri: MIXS:0000246 + - post + slot_uri: MIXS:0000079 multivalued: false - range: integer - required: false - recommended: false - window_size: - name: window_size + range: boolean + redox_potential: + name: redox_potential annotations: - Expected_value: - tag: Expected_value - value: measurement value Preferred_unit: tag: Preferred_unit - value: inch, meter - description: The window's length and width - title: window area/size + value: millivolt + description: Redox potential, measured relative to a hydrogen cell, indicating + oxidation or reduction potential + title: redox potential + examples: + - value: 300 millivolt from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - window - string_serialization: '{float} {unit} x {float} {unit}' - slot_uri: MIXS:0000224 + slot_uri: MIXS:0000182 multivalued: false + range: string required: false recommended: false - window_status: - name: window_status - description: Defines whether the windows were open or closed during environmental - testing - title: window status + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + ref_biomaterial: + name: ref_biomaterial + description: Primary publication if isolated before genome publication; otherwise, + primary genome report + title: reference for biomaterial examples: - - value: open + - value: doi:10.1016/j.syapm.2018.01.009 + in_subset: + - nucleic acid sequence source + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000025 + multivalued: false + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + ref_db: + name: ref_db + annotations: + Expected_value: + tag: Expected_value + value: names, versions, and references of databases + description: List of database(s) used for ORF annotation, along with version number + and reference to website or publication + title: reference database(s) + examples: + - value: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 + doi:10.1093/nar/gkw975 + in_subset: + - sequencing from_schema: https://w3id.org/mixs-6-2-rc keywords: - - status - - window - slot_uri: MIXS:0000855 + - database + string_serialization: '{database};{version};{reference}' + slot_uri: MIXS:0000062 multivalued: false - range: WINDOW_STATUS_ENUM - required: false - recommended: false - window_type: - name: window_type - description: The type of windows - title: window type + rel_air_humidity: + name: rel_air_humidity + annotations: + Preferred_unit: + tag: Preferred_unit + value: percentage + description: Partial vapor and air pressure, density of the vapor and air, or + by the actual mass of the vapor and air + title: relative air humidity + comments: + - percent or float? examples: - - value: fixed window + - value: '0.8' from_schema: https://w3id.org/mixs-6-2-rc keywords: - - type - - window - slot_uri: MIXS:0000856 + - air + - humidity + - relative + slot_uri: MIXS:0000121 + range: float + required: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + rel_humidity_out: + name: rel_humidity_out + annotations: + Preferred_unit: + tag: Preferred_unit + value: gram of air, kilogram of air + description: The recorded outside relative humidity value at the time of sampling + title: outside relative humidity + examples: + - value: 12 per kilogram of air + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - humidity + - relative + slot_uri: MIXS:0000188 multivalued: false - range: WINDOW_TYPE_ENUM + range: string required: false recommended: false - window_vert_pos: - name: window_vert_pos - description: The vertical position of the window on the wall - title: window vertical position + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + rel_location: + name: rel_location + description: Location of sampled soil to other parts of the farm e.g. under crop + plant, near irrigation ditch, from the dirt road + title: relative location of sample examples: - - value: middle + - value: furrow from_schema: https://w3id.org/mixs-6-2-rc keywords: - - window - slot_uri: MIXS:0000857 + - location + - relative + - sample + slot_uri: MIXS:0001161 multivalued: false - range: WINDOW_VERT_POS_ENUM - required: false - recommended: false - window_water_mold: - name: window_water_mold - description: Signs of the presence of mold or mildew on the window - title: window signs of water/mold + range: string + rel_samp_loc: + name: rel_samp_loc + description: The sampling location within the train car + title: relative sampling location examples: - - value: no presence of mold visible + - value: center of car from_schema: https://w3id.org/mixs-6-2-rc keywords: - - window - slot_uri: MIXS:0000854 + - location + - relative + slot_uri: MIXS:0000821 multivalued: false - range: SHARED_ENUM_1 + range: REL_SAMP_LOC_ENUM required: false recommended: false - x16s_recover: - name: x16s_recover - description: Can a 16S gene be recovered from the submitted SAG or MAG? - title: 16S recovered + rel_to_oxygen: + name: rel_to_oxygen + description: Is this organism an aerobe, anaerobe? Please note that aerobic and + anaerobic are valid descriptors for microbial environments + title: relationship to oxygen examples: - - value: 'yes' + - value: aerobe in_subset: - - sequencing + - nucleic acid sequence source from_schema: https://w3id.org/mixs-6-2-rc keywords: - - recover - slot_uri: MIXS:0000065 + - oxygen + - relationship + slot_uri: MIXS:0000015 multivalued: false - range: boolean - x16s_recover_software: - name: x16s_recover_software - description: Tools used for 16S rRNA gene extraction - title: 16S recovery software + range: REL_TO_OXYGEN_ENUM + repository_name: + name: repository_name + annotations: + Expected_value: + tag: Expected_value + value: Institution + description: The name of the institution where the sample or DNA extract is held + or "sample not available" if the sample was used in its entirety for analysis + or otherwise not retained + title: repository name examples: - - value: rambl;v2;default parameters - in_subset: - - sequencing + - value: FDA CFSAN Microbiology Laboratories from_schema: https://w3id.org/mixs-6-2-rc - keywords: - - recover - - software - slot_uri: MIXS:0000066 + string_serialization: '{text}' + slot_uri: MIXS:0001152 + multivalued: true + required: false + recommended: false + reservoir: + name: reservoir + description: Name of the reservoir (e.g. Carapebus) + title: reservoir name + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000303 multivalued: false range: string - pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + recommended: true + resins_pc: + name: resins_pc + annotations: + Preferred_unit: + tag: Preferred_unit + value: percent + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis + method that divides crude oil components according to their polarizability + and polarity. There are three main methods to obtain SARA results. The most + popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: + https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' + title: resins wt% + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000134 + multivalued: false + range: string + recommended: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: - syntax: ^{software};{version};{parameters}$ + syntax: ^{name};{float} {unit}$ interpolated: true partial_match: true - xylene: - name: xylene + room_air_exch_rate: + name: room_air_exch_rate annotations: Preferred_unit: tag: Preferred_unit - value: milligram per liter, parts per million - description: Concentration of xylene in the sample - title: xylene + value: liter per hour + description: The rate at which outside air replaces indoor air in a given space + title: room air exchange rate from_schema: https://w3id.org/mixs-6-2-rc - slot_uri: MIXS:0000156 + keywords: + - air + - rate + - room + slot_uri: MIXS:0000169 multivalued: false range: string - recommended: true + required: false + recommended: false pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ structured_pattern: syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ interpolated: true partial_match: true -classes: - MigsBa: - name: MigsBa - description: 'Minimal Information about a Genome Sequence: cultured bacteria/archaea' - title: MIGS bacteria + room_architec_elem: + name: room_architec_elem + description: The unique details and component parts that, together, form the architecture + of a distinguisahable space within a built structure + title: room architectural elements from_schema: https://w3id.org/mixs-6-2-rc - aliases: - - migs_ba - is_a: Checklist - mixin: true - slots: - - lat_lon - - lib_screen - - source_mat_id - - encoded_traits - - env_local_scale - - tax_class - - samp_vol_we_dna_ext - - nucl_acid_ext - - host_disease_stat - - elev - - seq_meth - - rel_to_oxygen - - adapters - - feat_pred - - assembly_qual - - ref_biomaterial - - extrachrom_elements - - alt - - ref_db - - compl_software - - assembly_name - - collection_date - - sim_search_meth - - temp - - biotic_relationship - - env_broad_scale - - samp_name - - host_spec_range - - num_replicons - - nucl_acid_amp - - lib_size - - isol_growth_condt - - depth - - annot - - lib_reads_seqd - - samp_collect_method - - experimental_factor - - project_name - - trophic_level - - samp_taxon_id - - assembly_software - - specific_host - - tax_ident - - number_contig - - env_medium - - pathogenicity - - samp_mat_process - - lib_layout - - compl_score - - geo_loc_name - - samp_collect_device - - pos_cont_type - - lib_vector - - neg_cont_type - - subspecf_gen_lin - - estimated_size - - samp_size - - associated_resource - - sop - slot_usage: - adapters: - name: adapters - recommended: true - alt: - name: alt - recommended: true - annot: - name: annot - recommended: true - assembly_name: - name: assembly_name - recommended: true - assembly_qual: - name: assembly_qual - required: true - assembly_software: - name: assembly_software - required: true - biotic_relationship: - name: biotic_relationship - recommended: true - compl_score: - name: compl_score - required: false - recommended: false - compl_software: - name: compl_software - required: false - recommended: false - depth: - name: depth - examples: - - value: 10 meter - recommended: true - elev: - name: elev - recommended: true - encoded_traits: - name: encoded_traits - required: false - recommended: false - estimated_size: - name: estimated_size - required: false - recommended: false - experimental_factor: - name: experimental_factor - required: false - recommended: false - extrachrom_elements: - name: extrachrom_elements - recommended: true - feat_pred: - name: feat_pred - required: false - recommended: false - host_disease_stat: - name: host_disease_stat - examples: - - value: rabies [DOID:11260] - recommended: true - host_spec_range: - name: host_spec_range - required: false - recommended: false - isol_growth_condt: - name: isol_growth_condt - required: true - lib_layout: - name: lib_layout - required: false - recommended: false - lib_reads_seqd: - name: lib_reads_seqd - required: false - recommended: false - lib_screen: - name: lib_screen - required: false - recommended: false - lib_size: - name: lib_size - required: false - recommended: false - lib_vector: - name: lib_vector - required: false - recommended: false - nucl_acid_amp: - name: nucl_acid_amp - recommended: true - nucl_acid_ext: - name: nucl_acid_ext - recommended: true - num_replicons: - name: num_replicons - required: true - number_contig: - name: number_contig - required: true - pathogenicity: - name: pathogenicity - recommended: true - ref_biomaterial: - name: ref_biomaterial - required: true - ref_db: - name: ref_db - required: false - recommended: false - rel_to_oxygen: - name: rel_to_oxygen - recommended: true - samp_collect_device: - name: samp_collect_device - examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] - required: false - recommended: false - samp_collect_method: - name: samp_collect_method - examples: - - value: swabbing - required: false - recommended: false - samp_mat_process: - name: samp_mat_process - required: false - recommended: false - samp_size: - name: samp_size - required: false - recommended: false - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - sim_search_meth: - name: sim_search_meth - required: false - recommended: false - sop: - name: sop - recommended: true - source_mat_id: - name: source_mat_id - recommended: true - specific_host: - name: specific_host - recommended: true - subspecf_gen_lin: - name: subspecf_gen_lin - recommended: true - tax_class: - name: tax_class - required: false - recommended: false - tax_ident: - name: tax_ident - recommended: true - temp: - name: temp - recommended: true - trophic_level: - name: trophic_level - recommended: true - class_uri: MIXS:0010003 - MigsEu: - name: MigsEu - description: 'Minimal Information about a Genome Sequence: eukaryote' - title: MIGS eukaryote + keywords: + - room + slot_uri: MIXS:0000233 + multivalued: false + range: string + required: false + recommended: false + room_condt: + name: room_condt + description: The condition of the room at the time of sampling + title: room condition + examples: + - value: new from_schema: https://w3id.org/mixs-6-2-rc - aliases: - - migs_eu - is_a: Checklist - mixin: true - slots: - - lat_lon - - lib_screen - - source_mat_id - - tax_class - - env_local_scale - - host_disease_stat - - samp_vol_we_dna_ext - - nucl_acid_ext - - elev - - seq_meth - - feat_pred - - adapters - - assembly_qual - - ref_biomaterial - - extrachrom_elements - - alt - - ref_db - - compl_software - - assembly_name - - propagation - - collection_date - - sim_search_meth - - temp - - biotic_relationship - - env_broad_scale - - host_spec_range - - samp_name - - num_replicons - - nucl_acid_amp - - lib_size - - isol_growth_condt - - depth - - annot - - lib_reads_seqd - - samp_collect_method - - experimental_factor - - project_name - - trophic_level - - samp_taxon_id - - assembly_software - - ploidy - - specific_host - - tax_ident - - number_contig - - env_medium - - pathogenicity - - samp_mat_process - - lib_layout - - compl_score - - geo_loc_name - - samp_collect_device - - pos_cont_type - - lib_vector - - neg_cont_type - - subspecf_gen_lin - - estimated_size - - samp_size - - associated_resource - - sop - slot_usage: - adapters: - name: adapters - recommended: true - alt: - name: alt - recommended: true - annot: - name: annot - recommended: true - assembly_name: - name: assembly_name - recommended: true - assembly_qual: - name: assembly_qual - required: true - assembly_software: - name: assembly_software - required: true - biotic_relationship: - name: biotic_relationship - required: false - recommended: false - compl_score: - name: compl_score - required: false - recommended: false - compl_software: - name: compl_software - required: false - recommended: false - depth: - name: depth - examples: - - value: 10 meter - recommended: true - elev: - name: elev - recommended: true - estimated_size: - name: estimated_size - required: false - recommended: false - experimental_factor: - name: experimental_factor - required: false - recommended: false - extrachrom_elements: - name: extrachrom_elements - required: false - recommended: false - feat_pred: - name: feat_pred - required: false - recommended: false - host_disease_stat: - name: host_disease_stat - examples: - - value: rabies [DOID:11260] - required: false - recommended: false - host_spec_range: - name: host_spec_range - required: false - recommended: false - isol_growth_condt: - name: isol_growth_condt - required: true - lib_layout: - name: lib_layout - required: false - recommended: false - lib_reads_seqd: - name: lib_reads_seqd - required: false - recommended: false - lib_screen: - name: lib_screen - required: false - recommended: false - lib_size: - name: lib_size - required: false - recommended: false - lib_vector: - name: lib_vector - required: false - recommended: false - nucl_acid_amp: - name: nucl_acid_amp - recommended: true - nucl_acid_ext: - name: nucl_acid_ext - recommended: true - num_replicons: - name: num_replicons - required: false - recommended: false - number_contig: - name: number_contig - required: true - pathogenicity: - name: pathogenicity - recommended: true - ploidy: - name: ploidy - required: false - recommended: false - propagation: - name: propagation - recommended: true - ref_biomaterial: - name: ref_biomaterial - required: false - recommended: false - ref_db: - name: ref_db - required: false - recommended: false - samp_collect_device: - name: samp_collect_device - examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] - required: false - recommended: false - samp_collect_method: - name: samp_collect_method - examples: - - value: swabbing - required: false - recommended: false - samp_mat_process: - name: samp_mat_process - required: false - recommended: false - samp_size: - name: samp_size - required: false - recommended: false - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - sim_search_meth: - name: sim_search_meth - required: false - recommended: false - sop: - name: sop - recommended: true - source_mat_id: - name: source_mat_id - recommended: true - specific_host: - name: specific_host - required: false - recommended: false - subspecf_gen_lin: - name: subspecf_gen_lin - recommended: true - tax_class: - name: tax_class - required: false - recommended: false - tax_ident: - name: tax_ident - recommended: true - temp: - name: temp - recommended: true - trophic_level: - name: trophic_level - recommended: true - class_uri: MIXS:0010002 - MigsOrg: - name: MigsOrg - description: 'Minimal Information about a Genome Sequence: organelle' - title: MIGS org + keywords: + - condition + - room + slot_uri: MIXS:0000822 + multivalued: false + range: ROOM_CONDT_ENUM + required: false + recommended: false + room_connected: + name: room_connected + description: List of rooms connected to the sampling room by a doorway + title: rooms connected by a doorway + examples: + - value: office from_schema: https://w3id.org/mixs-6-2-rc - aliases: - - migs_org - is_a: Checklist - mixin: true - slots: - - lat_lon - - lib_screen - - source_mat_id - - tax_class - - env_local_scale - - samp_vol_we_dna_ext - - nucl_acid_ext - - elev - - seq_meth - - feat_pred - - adapters - - assembly_qual - - ref_biomaterial - - extrachrom_elements - - alt - - ref_db - - compl_software - - assembly_name - - collection_date - - sim_search_meth - - temp - - env_broad_scale - - samp_name - - nucl_acid_amp - - lib_size - - depth - - annot - - lib_reads_seqd - - samp_collect_method - - experimental_factor - - project_name - - samp_taxon_id - - assembly_software - - tax_ident - - number_contig - - env_medium - - samp_mat_process - - lib_layout - - compl_score - - geo_loc_name - - estimated_size - - samp_collect_device - - pos_cont_type - - lib_vector - - neg_cont_type - - subspecf_gen_lin - - isol_growth_condt - - samp_size - - associated_resource - - sop - slot_usage: - adapters: - name: adapters - recommended: true - alt: - name: alt - recommended: true - annot: - name: annot - recommended: true - assembly_name: - name: assembly_name - recommended: true - assembly_qual: - name: assembly_qual - required: false - recommended: false - assembly_software: - name: assembly_software - required: true - compl_score: - name: compl_score - required: false - recommended: false - compl_software: - name: compl_software - required: false - recommended: false - depth: - name: depth - examples: - - value: 10 meter - recommended: true - elev: - name: elev - recommended: true - estimated_size: - name: estimated_size - required: false - recommended: false - experimental_factor: - name: experimental_factor - required: false - recommended: false - extrachrom_elements: - name: extrachrom_elements - recommended: true - feat_pred: - name: feat_pred - required: false - recommended: false - isol_growth_condt: - name: isol_growth_condt - required: true - lib_layout: - name: lib_layout - required: false - recommended: false - lib_reads_seqd: - name: lib_reads_seqd - required: false - recommended: false - lib_screen: - name: lib_screen - required: false - recommended: false - lib_size: - name: lib_size - required: false - recommended: false - lib_vector: - name: lib_vector - required: false - recommended: false - nucl_acid_amp: - name: nucl_acid_amp - recommended: true - nucl_acid_ext: - name: nucl_acid_ext - recommended: true - number_contig: - name: number_contig - required: false - recommended: false - ref_biomaterial: - name: ref_biomaterial - required: false - recommended: false - ref_db: - name: ref_db - required: false - recommended: false - samp_collect_device: - name: samp_collect_device - examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] - required: false - recommended: false - samp_collect_method: - name: samp_collect_method - examples: - - value: swabbing - required: false - recommended: false - samp_mat_process: - name: samp_mat_process - required: false - recommended: false - samp_size: - name: samp_size - required: false - recommended: false - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - sim_search_meth: - name: sim_search_meth - required: false - recommended: false - sop: - name: sop - recommended: true - source_mat_id: - name: source_mat_id - recommended: true - subspecf_gen_lin: - name: subspecf_gen_lin - recommended: true - tax_class: - name: tax_class - required: false - recommended: false - tax_ident: - name: tax_ident - recommended: true - temp: - name: temp - recommended: true - class_uri: MIXS:0010006 - MigsPl: - name: MigsPl - description: 'Minimal Information about a Genome Sequence: plasmid' - title: MIGS pl + keywords: + - doorway + - room + slot_uri: MIXS:0000826 + multivalued: false + range: ROOM_CONNECTED_ENUM + required: false + recommended: false + room_count: + name: room_count + description: The total count of rooms in the built structure including all room + types + title: room count from_schema: https://w3id.org/mixs-6-2-rc - aliases: - - migs_pl - is_a: Checklist - mixin: true - slots: - - lat_lon - - lib_screen - - source_mat_id - - encoded_traits - - env_local_scale - - tax_class - - samp_vol_we_dna_ext - - nucl_acid_ext - - elev - - seq_meth - - feat_pred - - adapters - - assembly_qual - - ref_biomaterial - - alt - - ref_db - - compl_software - - assembly_name - - propagation - - collection_date - - sim_search_meth - - temp - - env_broad_scale - - host_spec_range - - samp_name - - neg_cont_type - - nucl_acid_amp - - lib_size - - isol_growth_condt - - depth - - annot - - lib_reads_seqd - - samp_collect_method - - experimental_factor - - project_name - - samp_taxon_id - - assembly_software - - specific_host - - tax_ident - - number_contig - - env_medium - - samp_mat_process - - lib_layout - - compl_score - - geo_loc_name - - pos_cont_type - - lib_vector - - samp_collect_device - - subspecf_gen_lin - - estimated_size - - samp_size - - associated_resource - - sop - slot_usage: - adapters: - name: adapters - recommended: true - alt: - name: alt - recommended: true - annot: - name: annot - recommended: true - assembly_name: - name: assembly_name - recommended: true - assembly_qual: - name: assembly_qual - required: false - recommended: false - assembly_software: - name: assembly_software - required: true - compl_score: - name: compl_score - required: false - recommended: false - compl_software: - name: compl_software - required: false - recommended: false - depth: - name: depth - examples: - - value: 10 meter - recommended: true - elev: - name: elev - recommended: true - encoded_traits: - name: encoded_traits - recommended: true - estimated_size: - name: estimated_size - required: false - recommended: false - experimental_factor: - name: experimental_factor - required: false - recommended: false - feat_pred: - name: feat_pred - required: false - recommended: false - host_spec_range: - name: host_spec_range - required: false - recommended: false - isol_growth_condt: - name: isol_growth_condt - required: true - lib_layout: - name: lib_layout - required: false - recommended: false - lib_reads_seqd: - name: lib_reads_seqd - required: false - recommended: false - lib_screen: - name: lib_screen - required: false - recommended: false - lib_size: - name: lib_size - required: false - recommended: false - lib_vector: - name: lib_vector - required: false - recommended: false - nucl_acid_amp: - name: nucl_acid_amp - recommended: true - nucl_acid_ext: - name: nucl_acid_ext - recommended: true - number_contig: - name: number_contig - required: false - recommended: false - propagation: - name: propagation - required: true - ref_biomaterial: - name: ref_biomaterial - required: false - recommended: false - ref_db: - name: ref_db - required: false - recommended: false - samp_collect_device: - name: samp_collect_device - examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] - required: false - recommended: false - samp_collect_method: - name: samp_collect_method - examples: - - value: swabbing - required: false - recommended: false - samp_mat_process: - name: samp_mat_process - required: false - recommended: false - samp_size: - name: samp_size - required: false - recommended: false - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - sim_search_meth: - name: sim_search_meth - required: false - recommended: false - sop: - name: sop - recommended: true - source_mat_id: - name: source_mat_id - recommended: true - specific_host: - name: specific_host - recommended: true - subspecf_gen_lin: - name: subspecf_gen_lin - recommended: true - tax_class: - name: tax_class - required: false - recommended: false - tax_ident: - name: tax_ident - recommended: true - temp: - name: temp - recommended: true - class_uri: MIXS:0010004 - MigsVi: - name: MigsVi - description: 'Minimal Information about a Genome Sequence: virus' - title: MIGS virus + keywords: + - count + - room + slot_uri: MIXS:0000234 + multivalued: false + range: integer + required: false + recommended: false + room_dim: + name: room_dim + annotations: + Expected_value: + tag: Expected_value + value: measurement value + Preferred_unit: + tag: Preferred_unit + value: meter + description: The length, width and height of sampling room + title: room dimensions + examples: + - value: 4 meter x 4 meter x 4 meter from_schema: https://w3id.org/mixs-6-2-rc - aliases: - - migs_vi - is_a: Checklist - mixin: true - slots: - - lat_lon - - lib_screen - - source_mat_id - - encoded_traits - - env_local_scale - - tax_class - - samp_vol_we_dna_ext - - nucl_acid_ext - - elev - - seq_meth - - feat_pred - - adapters - - assembly_qual - - ref_biomaterial - - alt - - ref_db - - compl_software - - assembly_name - - propagation - - sim_search_meth - - temp - - biotic_relationship - - env_broad_scale - - host_spec_range - - samp_name - - num_replicons - - nucl_acid_amp - - lib_size - - neg_cont_type - - samp_size - - depth - - annot - - lib_reads_seqd - - samp_collect_method - - experimental_factor - - virus_enrich_appr - - project_name - - samp_taxon_id - - assembly_software - - specific_host - - tax_ident - - number_contig - - env_medium - - pathogenicity - - samp_mat_process - - lib_layout - - compl_score - - geo_loc_name - - estimated_size - - samp_collect_device - - pos_cont_type - - lib_vector - - isol_growth_condt - - subspecf_gen_lin - - host_disease_stat - - collection_date - - associated_resource - - sop - slot_usage: - adapters: - name: adapters - recommended: true - alt: - name: alt - recommended: true - annot: - name: annot - recommended: true - assembly_name: - name: assembly_name - recommended: true - assembly_qual: - name: assembly_qual - required: false - recommended: false - assembly_software: - name: assembly_software - required: true - biotic_relationship: - name: biotic_relationship - required: false - recommended: false - compl_score: - name: compl_score - required: false - recommended: false - compl_software: - name: compl_software - required: false - recommended: false - depth: - name: depth - examples: - - value: 10 meter - recommended: true - elev: - name: elev - recommended: true - encoded_traits: - name: encoded_traits - recommended: true - estimated_size: - name: estimated_size - required: false - recommended: false - experimental_factor: - name: experimental_factor - required: false - recommended: false - feat_pred: - name: feat_pred - required: false - recommended: false - host_disease_stat: - name: host_disease_stat - examples: - - value: rabies [DOID:11260] - recommended: true - host_spec_range: - name: host_spec_range - recommended: true - isol_growth_condt: - name: isol_growth_condt - required: true - lib_layout: - name: lib_layout - required: false - recommended: false - lib_reads_seqd: - name: lib_reads_seqd - required: false - recommended: false - lib_screen: - name: lib_screen - required: false - recommended: false - lib_size: - name: lib_size - required: false - recommended: false - lib_vector: - name: lib_vector - required: false - recommended: false - nucl_acid_amp: - name: nucl_acid_amp - recommended: true - nucl_acid_ext: - name: nucl_acid_ext - recommended: true - num_replicons: - name: num_replicons - recommended: true - number_contig: - name: number_contig - required: false - recommended: false - pathogenicity: - name: pathogenicity - recommended: true - propagation: - name: propagation - required: true - ref_biomaterial: - name: ref_biomaterial - required: false - recommended: false - ref_db: - name: ref_db - required: false - recommended: false - samp_collect_device: - name: samp_collect_device - examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] - required: false - recommended: false - samp_collect_method: - name: samp_collect_method - examples: - - value: swabbing - required: false - recommended: false - samp_mat_process: - name: samp_mat_process - required: false - recommended: false - samp_size: - name: samp_size - required: false - recommended: false - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - sim_search_meth: - name: sim_search_meth - required: false - recommended: false - sop: - name: sop - recommended: true - source_mat_id: - name: source_mat_id - recommended: true - specific_host: - name: specific_host - recommended: true - subspecf_gen_lin: - name: subspecf_gen_lin - recommended: true - tax_class: - name: tax_class - required: false - recommended: false - tax_ident: - name: tax_ident - recommended: true - temp: - name: temp - recommended: true - virus_enrich_appr: - name: virus_enrich_appr - recommended: true - class_uri: MIXS:0010005 - Mimag: - name: Mimag - description: Minimum Information About a Metagenome-Assembled Genome - title: MIMAG + keywords: + - dimensions + - room + string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}' + slot_uri: MIXS:0000192 + multivalued: false + required: false + recommended: false + room_door_dist: + name: room_door_dist + annotations: + Preferred_unit: + tag: Preferred_unit + value: meter + description: Distance between doors (meters) in the hallway between the sampling + room and adjacent rooms + title: room door distance from_schema: https://w3id.org/mixs-6-2-rc - aliases: - - mimag - is_a: Checklist - mixin: true - slots: - - bin_software - - lat_lon - - x16s_recover_software - - lib_screen - - source_mat_id - - tax_class - - env_local_scale - - samp_vol_we_dna_ext - - nucl_acid_ext - - elev - - seq_meth - - rel_to_oxygen - - adapters - - feat_pred - - assembly_qual - - ref_biomaterial - - alt - - mid - - ref_db - - x16s_recover - - compl_software - - assembly_name - - collection_date - - contam_screen_param - - sim_search_meth - - reassembly_bin - - temp - - env_broad_scale - - samp_name - - trnas - - nucl_acid_amp - - lib_size - - bin_param - - trna_ext_software - - depth - - compl_appr - - annot - - lib_reads_seqd - - samp_collect_method - - experimental_factor - - size_frac - - project_name - - samp_taxon_id - - assembly_software - - tax_ident - - number_contig - - env_medium - - contam_score - - samp_mat_process - - lib_layout - - compl_score - - geo_loc_name - - mag_cov_software - - samp_collect_device - - pos_cont_type - - lib_vector - - neg_cont_type - - decontam_software - - contam_screen_input - - samp_size - - associated_resource - - sop - slot_usage: - adapters: - name: adapters - recommended: true - alt: - name: alt - recommended: true - annot: - name: annot - required: false - recommended: false - assembly_name: - name: assembly_name - recommended: true - assembly_qual: - name: assembly_qual - required: true - assembly_software: - name: assembly_software - required: true - bin_param: - name: bin_param - required: true - bin_software: - name: bin_software - required: true - compl_appr: - name: compl_appr - required: false - recommended: false - compl_score: - name: compl_score - required: true - compl_software: - name: compl_software - required: true - contam_score: - name: contam_score - required: true - contam_screen_input: - name: contam_screen_input - required: false - recommended: false - contam_screen_param: - name: contam_screen_param - required: false - recommended: false - decontam_software: - name: decontam_software - required: false - recommended: false - depth: - name: depth - examples: - - value: 10 meter - recommended: true - elev: - name: elev - recommended: true - experimental_factor: - name: experimental_factor - recommended: true - feat_pred: - name: feat_pred - required: false - recommended: false - lib_layout: - name: lib_layout - recommended: true - lib_reads_seqd: - name: lib_reads_seqd - recommended: true - lib_screen: - name: lib_screen - recommended: true - lib_size: - name: lib_size - recommended: true - lib_vector: - name: lib_vector - recommended: true - mag_cov_software: - name: mag_cov_software - required: false - recommended: false - mid: - name: mid - recommended: true - nucl_acid_amp: - name: nucl_acid_amp - recommended: true - nucl_acid_ext: - name: nucl_acid_ext - recommended: true - number_contig: - name: number_contig - required: false - recommended: false - reassembly_bin: - name: reassembly_bin - required: false - recommended: false - ref_biomaterial: - name: ref_biomaterial - required: false - recommended: false - ref_db: - name: ref_db - required: false - recommended: false - rel_to_oxygen: - name: rel_to_oxygen - required: false - recommended: false - samp_collect_device: - name: samp_collect_device - examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] - recommended: true - samp_collect_method: - name: samp_collect_method - examples: - - value: swabbing - recommended: true - samp_mat_process: - name: samp_mat_process - recommended: true - samp_size: - name: samp_size - recommended: true - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - sim_search_meth: - name: sim_search_meth - required: false - recommended: false - size_frac: - name: size_frac - required: false - recommended: false - sop: - name: sop - recommended: true - source_mat_id: - name: source_mat_id - recommended: true - tax_class: - name: tax_class - required: false - recommended: false - tax_ident: - name: tax_ident - required: true - temp: - name: temp - recommended: true - trna_ext_software: - name: trna_ext_software - required: false - recommended: false - trnas: - name: trnas - required: false - recommended: false - x16s_recover: - name: x16s_recover - required: false - recommended: false - x16s_recover_software: - name: x16s_recover_software - required: false - recommended: false - class_uri: MIXS:0010011 - MimarksC: - name: MimarksC - description: 'Minimal Information about a Marker Specimen: specimen' - title: MIMARKS specimen - comments: - - for marker gene sequences from cultured or voucher-identifiable specimens + keywords: + - distance + - door + - room + slot_uri: MIXS:0000193 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + room_door_share: + name: room_door_share + description: List of room(s) (room number, room name) sharing a door with the + sampling room + title: rooms that share a door with sampling room from_schema: https://w3id.org/mixs-6-2-rc - aliases: - - mimarks_c - - MIMARKS-SU - - MIMARKS-specimen - is_a: Checklist - mixin: true - slots: - - lat_lon - - chimera_check - - source_mat_id - - env_local_scale - - samp_vol_we_dna_ext - - nucl_acid_ext - - elev - - seq_meth - - rel_to_oxygen - - extrachrom_elements - - alt - - pcr_primers - - pcr_cond - - temp - - biotic_relationship - - env_broad_scale - - samp_name - - samp_size - - nucl_acid_amp - - seq_quality_check - - depth - - samp_collect_method - - experimental_factor - - project_name - - trophic_level - - samp_taxon_id - - env_medium - - samp_mat_process - - geo_loc_name - - target_gene - - samp_collect_device - - pos_cont_type - - target_subfragment - - neg_cont_type - - subspecf_gen_lin - - isol_growth_condt - - collection_date - - associated_resource - - sop - slot_usage: - alt: - name: alt - recommended: true - biotic_relationship: - name: biotic_relationship - recommended: true - chimera_check: - name: chimera_check - recommended: true - depth: - name: depth - examples: - - value: 10 meter - recommended: true - elev: - name: elev - recommended: true - experimental_factor: - name: experimental_factor - required: false - recommended: false - extrachrom_elements: - name: extrachrom_elements - required: false - recommended: false - isol_growth_condt: - name: isol_growth_condt - required: true - nucl_acid_amp: - name: nucl_acid_amp - recommended: true - nucl_acid_ext: - name: nucl_acid_ext - recommended: true - pcr_cond: - name: pcr_cond - recommended: true - pcr_primers: - name: pcr_primers - recommended: true - rel_to_oxygen: - name: rel_to_oxygen - recommended: true - samp_collect_device: - name: samp_collect_device - examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] - required: false - recommended: false - samp_collect_method: - name: samp_collect_method - examples: - - value: swabbing - required: false - recommended: false - samp_mat_process: - name: samp_mat_process - recommended: true - samp_size: - name: samp_size - required: false - recommended: false - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - seq_quality_check: - name: seq_quality_check - recommended: true - sop: - name: sop - recommended: true - source_mat_id: - name: source_mat_id - recommended: true - subspecf_gen_lin: - name: subspecf_gen_lin - recommended: true - target_gene: - name: target_gene - required: true - target_subfragment: - name: target_subfragment - recommended: true - temp: - name: temp - recommended: true - trophic_level: - name: trophic_level - recommended: true - class_uri: MIXS:0010009 - MimarksS: - name: MimarksS - description: 'Minimal Information about a Marker Specimen: survey' - title: MIMARKS survey - comments: - - for marker gene sequences obtained directly from the environment - from_schema: https://w3id.org/mixs-6-2-rc - aliases: - - mimarks_s - - MIMARKS-SP - - MIMARKS-survey - is_a: Checklist - mixin: true - slots: - - lat_lon - - lib_screen - - source_mat_id - - chimera_check - - env_local_scale - - samp_vol_we_dna_ext - - nucl_acid_ext - - elev - - seq_meth - - rel_to_oxygen - - adapters - - alt - - mid - - collection_date - - pcr_primers - - pcr_cond - - temp - - env_broad_scale - - samp_name - - nucl_acid_amp - - lib_size - - seq_quality_check - - depth - - lib_reads_seqd - - samp_collect_method - - experimental_factor - - size_frac - - project_name - - samp_taxon_id - - assembly_software - - env_medium - - samp_mat_process - - lib_layout - - geo_loc_name - - target_gene - - lib_vector - - samp_collect_device - - pos_cont_type - - target_subfragment - - neg_cont_type - - samp_size - - associated_resource - - sop - slot_usage: - adapters: - name: adapters - recommended: true - alt: - name: alt - recommended: true - assembly_software: - name: assembly_software - recommended: true - chimera_check: - name: chimera_check - recommended: true - depth: - name: depth - examples: - - value: 10 meter - recommended: true - elev: - name: elev - recommended: true - experimental_factor: - name: experimental_factor - recommended: true - lib_layout: - name: lib_layout - recommended: true - lib_reads_seqd: - name: lib_reads_seqd - recommended: true - lib_screen: - name: lib_screen - recommended: true - lib_size: - name: lib_size - recommended: true - lib_vector: - name: lib_vector - recommended: true - mid: - name: mid - recommended: true - nucl_acid_amp: - name: nucl_acid_amp - recommended: true - nucl_acid_ext: - name: nucl_acid_ext - recommended: true - pcr_cond: - name: pcr_cond - recommended: true - pcr_primers: - name: pcr_primers - recommended: true - rel_to_oxygen: - name: rel_to_oxygen - required: false - recommended: false - samp_collect_device: - name: samp_collect_device - examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] - recommended: true - samp_collect_method: - name: samp_collect_method - examples: - - value: swabbing - recommended: true - samp_mat_process: - name: samp_mat_process - recommended: true - samp_size: - name: samp_size - recommended: true - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - seq_quality_check: - name: seq_quality_check - recommended: true - size_frac: - name: size_frac - required: false - recommended: false - sop: - name: sop - recommended: true - source_mat_id: - name: source_mat_id - recommended: true - target_gene: - name: target_gene - required: true - target_subfragment: - name: target_subfragment - recommended: true - temp: - name: temp - recommended: true - class_uri: MIXS:0010008 - Mims: - name: Mims - description: Metagenome or Environmental - title: MIMS + keywords: + - door + - room + slot_uri: MIXS:0000242 + multivalued: false + range: string + required: false + recommended: false + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ + structured_pattern: + syntax: ^{room_name};{room_number}$ + interpolated: true + partial_match: true + room_hallway: + name: room_hallway + description: List of room(s) (room number, room name) located in the same hallway + as sampling room + title: rooms that are on the same hallway from_schema: https://w3id.org/mixs-6-2-rc - aliases: - - mims - is_a: Checklist - mixin: true - slots: - - lat_lon - - lib_screen - - source_mat_id - - tax_class - - env_local_scale - - samp_vol_we_dna_ext - - nucl_acid_ext - - elev - - seq_meth - - rel_to_oxygen - - adapters - - feat_pred - - assembly_qual - - ref_biomaterial - - alt - - mid - - ref_db - - assembly_name - - collection_date - - sim_search_meth - - temp - - env_broad_scale - - samp_name - - nucl_acid_amp - - lib_size - - depth - - annot - - lib_reads_seqd - - samp_collect_method - - experimental_factor - - size_frac - - project_name - - samp_taxon_id - - assembly_software - - number_contig - - env_medium - - samp_mat_process - - lib_layout - - geo_loc_name - - samp_collect_device - - pos_cont_type - - lib_vector - - neg_cont_type - - samp_size - - associated_resource - - sop - slot_usage: - adapters: - name: adapters - recommended: true - alt: - name: alt - recommended: true - annot: - name: annot - recommended: true - assembly_name: - name: assembly_name - recommended: true - assembly_qual: - name: assembly_qual - recommended: true - assembly_software: - name: assembly_software - recommended: true - depth: - name: depth - examples: - - value: 10 meter - recommended: true - elev: - name: elev - recommended: true - experimental_factor: - name: experimental_factor - recommended: true - feat_pred: - name: feat_pred - required: false - recommended: false - lib_layout: - name: lib_layout - recommended: true - lib_reads_seqd: - name: lib_reads_seqd - recommended: true - lib_screen: - name: lib_screen - recommended: true - lib_size: - name: lib_size - recommended: true - lib_vector: - name: lib_vector - recommended: true - mid: - name: mid - recommended: true - nucl_acid_amp: - name: nucl_acid_amp - recommended: true - nucl_acid_ext: - name: nucl_acid_ext - recommended: true - number_contig: - name: number_contig - recommended: true - ref_biomaterial: - name: ref_biomaterial - required: false - recommended: false - ref_db: - name: ref_db - required: false - recommended: false - rel_to_oxygen: - name: rel_to_oxygen - required: false - recommended: false - samp_collect_device: - name: samp_collect_device - examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] - recommended: true - samp_collect_method: - name: samp_collect_method - examples: - - value: swabbing - recommended: true - samp_mat_process: - name: samp_mat_process - recommended: true - samp_size: - name: samp_size - recommended: true - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - sim_search_meth: - name: sim_search_meth - required: false - recommended: false - size_frac: - name: size_frac - required: false - recommended: false - sop: - name: sop - recommended: true - source_mat_id: - name: source_mat_id - recommended: true - tax_class: - name: tax_class - required: false - recommended: false - temp: - name: temp - recommended: true - class_uri: MIXS:0010007 - Misag: - name: Misag - description: Minimum Information About a Single Amplified Genome - title: Minimum Information About a Single Amplified Genome + keywords: + - hallway + - room + slot_uri: MIXS:0000238 + multivalued: false + range: string + required: false + recommended: false + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ + structured_pattern: + syntax: ^{room_name};{room_number}$ + interpolated: true + partial_match: true + room_loc: + name: room_loc + description: The position of the room within the building + title: room location in building + examples: + - value: interior room from_schema: https://w3id.org/mixs-6-2-rc - aliases: - - misag - is_a: Checklist - mixin: true - slots: - - lat_lon - - x16s_recover_software - - lib_screen - - source_mat_id - - tax_class - - env_local_scale - - samp_vol_we_dna_ext - - nucl_acid_ext - - elev - - seq_meth - - rel_to_oxygen - - adapters - - feat_pred - - assembly_qual - - ref_biomaterial - - alt - - mid - - ref_db - - x16s_recover - - compl_software - - wga_amp_kit - - assembly_name - - contam_screen_param - - sim_search_meth - - temp - - env_broad_scale - - samp_name - - trnas - - neg_cont_type - - nucl_acid_amp - - lib_size - - samp_size - - trna_ext_software - - depth - - compl_appr - - annot - - lib_reads_seqd - - samp_collect_method - - experimental_factor - - size_frac - - sc_lysis_approach - - sort_tech - - project_name - - samp_taxon_id - - assembly_software - - sc_lysis_method - - tax_ident - - number_contig - - env_medium - - wga_amp_appr - - contam_score - - samp_mat_process - - lib_layout - - compl_score - - geo_loc_name - - pos_cont_type - - lib_vector - - samp_collect_device - - decontam_software - - contam_screen_input - - collection_date - - associated_resource - - sop - slot_usage: - adapters: - name: adapters - recommended: true - alt: - name: alt - recommended: true - annot: - name: annot - required: false - recommended: false - assembly_name: - name: assembly_name - recommended: true - assembly_qual: - name: assembly_qual - required: true - assembly_software: - name: assembly_software - required: true - compl_appr: - name: compl_appr - required: false - recommended: false - compl_score: - name: compl_score - required: true - compl_software: - name: compl_software - required: true - contam_score: - name: contam_score - required: true - contam_screen_input: - name: contam_screen_input - required: false - recommended: false - contam_screen_param: - name: contam_screen_param - required: false - recommended: false - decontam_software: - name: decontam_software - required: false - recommended: false - depth: - name: depth - examples: - - value: 10 meter - recommended: true - elev: - name: elev - recommended: true - experimental_factor: - name: experimental_factor - recommended: true - feat_pred: - name: feat_pred - required: false - recommended: false - lib_layout: - name: lib_layout - recommended: true - lib_reads_seqd: - name: lib_reads_seqd - recommended: true - lib_screen: - name: lib_screen - recommended: true - lib_size: - name: lib_size - recommended: true - lib_vector: - name: lib_vector - recommended: true - mid: - name: mid - recommended: true - nucl_acid_amp: - name: nucl_acid_amp - recommended: true - nucl_acid_ext: - name: nucl_acid_ext - recommended: true - number_contig: - name: number_contig - required: false - recommended: false - ref_biomaterial: - name: ref_biomaterial - required: false - recommended: false - ref_db: - name: ref_db - required: false - recommended: false - rel_to_oxygen: - name: rel_to_oxygen - required: false - recommended: false - samp_collect_device: - name: samp_collect_device - examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] - recommended: true - samp_collect_method: - name: samp_collect_method - examples: - - value: swabbing - recommended: true - samp_mat_process: - name: samp_mat_process - recommended: true - samp_size: - name: samp_size - recommended: true - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - sc_lysis_approach: - name: sc_lysis_approach - required: true - sc_lysis_method: - name: sc_lysis_method - required: false - recommended: false - sim_search_meth: - name: sim_search_meth - required: false - recommended: false - size_frac: - name: size_frac - required: false - recommended: false - sop: - name: sop - recommended: true - sort_tech: - name: sort_tech - required: true - source_mat_id: - name: source_mat_id - recommended: true - tax_class: - name: tax_class - required: false - recommended: false - tax_ident: - name: tax_ident - required: true - temp: - name: temp - recommended: true - trna_ext_software: - name: trna_ext_software - required: false - recommended: false - trnas: - name: trnas - required: false - recommended: false - wga_amp_appr: - name: wga_amp_appr - required: true - wga_amp_kit: - name: wga_amp_kit - required: false - recommended: false - x16s_recover: - name: x16s_recover - required: false - recommended: false - x16s_recover_software: - name: x16s_recover_software - required: false - recommended: false - class_uri: MIXS:0010010 - Miuvig: - name: Miuvig - description: Minimum Information About an Uncultivated Virus Genome - title: Minimum Information About an Uncultivated Virus Genome + keywords: + - location + - room + slot_uri: MIXS:0000823 + multivalued: false + range: ROOM_LOC_ENUM + required: false + recommended: false + room_moist_dam_hist: + name: room_moist_dam_hist + description: The history of moisture damage or mold in the past 12 months. Number + of events of moisture damage or mold observed + title: room moisture damage or mold history from_schema: https://w3id.org/mixs-6-2-rc - aliases: - - miuvig - is_a: Checklist - mixin: true - slots: - - lat_lon - - lib_screen - - source_mat_id - - tax_class - - env_local_scale - - samp_vol_we_dna_ext - - nucl_acid_ext - - elev - - seq_meth - - feat_pred - - adapters - - assembly_qual - - ref_biomaterial - - alt - - mid - - ref_db - - compl_software - - assembly_name - - collection_date - - sim_search_meth - - temp - - biotic_relationship - - env_broad_scale - - host_spec_range - - samp_name - - trnas - - nucl_acid_amp - - lib_size - - neg_cont_type - - trna_ext_software - - depth - - source_uvig - - compl_appr - - annot - - lib_reads_seqd - - samp_collect_method - - experimental_factor - - size_frac - - virus_enrich_appr - - project_name - - samp_taxon_id - - assembly_software - - specific_host - - tax_ident - - number_contig - - env_medium - - pathogenicity - - samp_mat_process - - lib_layout - - compl_score - - geo_loc_name - - estimated_size - - pos_cont_type - - lib_vector - - samp_collect_device - - host_disease_stat - - samp_size - - sort_tech - - sc_lysis_approach - - sc_lysis_method - - wga_amp_appr - - wga_amp_kit - - bin_param - - bin_software - - reassembly_bin - - mag_cov_software - - vir_ident_software - - pred_genome_type - - pred_genome_struc - - detec_type - - otu_class_appr - - otu_seq_comp_appr - - otu_db - - host_pred_appr - - host_pred_est_acc - - associated_resource - - sop - slot_usage: - adapters: - name: adapters - recommended: true - alt: - name: alt - recommended: true - annot: - name: annot - required: false - recommended: false - assembly_name: - name: assembly_name - recommended: true - assembly_qual: - name: assembly_qual - required: true - assembly_software: - name: assembly_software - required: true - bin_param: - name: bin_param - recommended: true - bin_software: - name: bin_software - recommended: true - biotic_relationship: - name: biotic_relationship - required: false - recommended: false - compl_appr: - name: compl_appr - recommended: true - compl_score: - name: compl_score - recommended: true - compl_software: - name: compl_software - required: false - recommended: false - depth: - name: depth - examples: - - value: 10 meter - recommended: true - detec_type: - name: detec_type - required: true - elev: - name: elev - recommended: true - estimated_size: - name: estimated_size - required: false - recommended: false - experimental_factor: - name: experimental_factor - recommended: true - feat_pred: - name: feat_pred - recommended: true - host_disease_stat: - name: host_disease_stat - examples: - - value: rabies [DOID:11260] - recommended: true - host_pred_appr: - name: host_pred_appr - recommended: true - host_pred_est_acc: - name: host_pred_est_acc - recommended: true - host_spec_range: - name: host_spec_range - required: false - recommended: false - lib_layout: - name: lib_layout - recommended: true - lib_reads_seqd: - name: lib_reads_seqd - recommended: true - lib_screen: - name: lib_screen - recommended: true - lib_size: - name: lib_size - recommended: true - lib_vector: - name: lib_vector - recommended: true - mag_cov_software: - name: mag_cov_software - required: false - recommended: false - mid: - name: mid - recommended: true - nucl_acid_amp: - name: nucl_acid_amp - recommended: true - nucl_acid_ext: - name: nucl_acid_ext - recommended: true - number_contig: - name: number_contig - required: true - otu_class_appr: - name: otu_class_appr - recommended: true - otu_db: - name: otu_db - recommended: true - otu_seq_comp_appr: - name: otu_seq_comp_appr - recommended: true - pathogenicity: - name: pathogenicity - required: false - recommended: false - pred_genome_struc: - name: pred_genome_struc - required: true - pred_genome_type: - name: pred_genome_type - required: true - reassembly_bin: - name: reassembly_bin - recommended: true - ref_biomaterial: - name: ref_biomaterial - required: false - recommended: false - ref_db: - name: ref_db - recommended: true - samp_collect_device: - name: samp_collect_device - examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] - recommended: true - samp_collect_method: - name: samp_collect_method - examples: - - value: swabbing - recommended: true - samp_mat_process: - name: samp_mat_process - recommended: true - samp_size: - name: samp_size - recommended: true - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - sc_lysis_approach: - name: sc_lysis_approach - recommended: true - sc_lysis_method: - name: sc_lysis_method - recommended: true - sim_search_meth: - name: sim_search_meth - recommended: true - size_frac: - name: size_frac - recommended: true - sop: - name: sop - recommended: true - sort_tech: - name: sort_tech - recommended: true - source_mat_id: - name: source_mat_id - recommended: true - source_uvig: - name: source_uvig - required: true - specific_host: - name: specific_host - required: false - recommended: false - tax_class: - name: tax_class - recommended: true - tax_ident: - name: tax_ident - required: false - recommended: false - temp: - name: temp - recommended: true - trna_ext_software: - name: trna_ext_software - required: false - recommended: false - trnas: - name: trnas - required: false - recommended: false - vir_ident_software: - name: vir_ident_software - required: true - virus_enrich_appr: - name: virus_enrich_appr - required: true - wga_amp_appr: - name: wga_amp_appr - recommended: true - wga_amp_kit: - name: wga_amp_kit - recommended: true - class_uri: MIXS:0010012 - Agriculture: - name: Agriculture - description: agriculture extension - title: agriculture + keywords: + - history + - moisture + - room + slot_uri: MIXS:0000235 + multivalued: false + range: integer + required: false + recommended: false + room_net_area: + name: room_net_area + annotations: + Preferred_unit: + tag: Preferred_unit + value: square feet, square meter + description: The net floor area of sampling room. Net area excludes wall thicknesses + title: room net area from_schema: https://w3id.org/mixs-6-2-rc - is_a: Extension - slots: - - plant_growth_med - - photosynt_activ - - photosynt_activ_meth - - samp_collect_method + keywords: + - area + - room + slot_uri: MIXS:0000194 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + room_occup: + name: room_occup + description: Count of room occupancy at time of sampling + title: room occupancy + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - room + slot_uri: MIXS:0000236 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + room_samp_pos: + name: room_samp_pos + description: The horizontal sampling position in the room relative to architectural + elements + title: room sampling position + examples: + - value: south corner + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - room + slot_uri: MIXS:0000824 + multivalued: false + range: ROOM_SAMP_POS_ENUM + required: false + recommended: false + room_type: + name: room_type + annotations: + Expected_value: + tag: Expected_value + value: enumeration + description: The main purpose or activity of the sampling room. A room is any + distinguishable space within a structure + title: room type + examples: + - value: bathroom + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - room + - type + string_serialization: '[attic|bathroom|closet|conference room|elevator|examining + room|hallway|kitchen|mail room|private office|open office|stairwell|,restroom|lobby|vestibule|mechanical + or electrical room|data center|laboratory_wet|laboratory_dry|gymnasium|natatorium|auditorium|lockers|cafe|warehouse]' + slot_uri: MIXS:0000825 + multivalued: false + required: false + recommended: false + room_vol: + name: room_vol + annotations: + Preferred_unit: + tag: Preferred_unit + value: cubic feet, cubic meter + description: Volume of sampling room + title: room volume + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - room + - volume + slot_uri: MIXS:0000195 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{integer} {text}$ + interpolated: true + partial_match: true + room_wall_share: + name: room_wall_share + description: List of room(s) (room number, room name) sharing a wall with the + sampling room + title: rooms that share a wall with sampling room + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - room + - wall + slot_uri: MIXS:0000243 + multivalued: false + range: string + required: false + recommended: false + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[1-9][0-9]*$ + structured_pattern: + syntax: ^{room_name};{room_number}$ + interpolated: true + partial_match: true + room_window_count: + name: room_window_count + description: Number of windows in the room + title: room window count + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - count + - room + - window + slot_uri: MIXS:0000237 + multivalued: false + range: integer + required: false + recommended: false + root_cond: + name: root_cond + description: Relevant rooting conditions such as field plot size, sowing density, + container dimensions, number of plants per container + title: rooting conditions + examples: + - value: http://himedialabs.com/TD/PT158.pdf + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - condition + slot_uri: MIXS:0001061 + multivalued: false + range: string + required: false + recommended: false + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}|{text}$ + interpolated: true + partial_match: true + root_med_carbon: + name: root_med_carbon + annotations: + Expected_value: + tag: Expected_value + value: carbon source name;measurement value + Preferred_unit: + tag: Preferred_unit + value: milligram per liter + description: Source of organic carbon in the culture rooting medium; e.g. sucrose + title: rooting medium carbon + examples: + - value: sucrose + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - carbon + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000577 + multivalued: false + required: false + recommended: false + root_med_macronutr: + name: root_med_macronutr + annotations: + Expected_value: + tag: Expected_value + value: macronutrient name;measurement value + Preferred_unit: + tag: Preferred_unit + value: milligram per liter + description: Measurement of the culture rooting medium macronutrients (N,P, K, + Ca, Mg, S); e.g. KH2PO4 (170 mg/L) + title: rooting medium macronutrients + examples: + - value: KH2PO4;170 milligram per liter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - macronutrients + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000578 + multivalued: false + required: false + recommended: false + root_med_micronutr: + name: root_med_micronutr + annotations: + Expected_value: + tag: Expected_value + value: micronutrient name;measurement value + Preferred_unit: + tag: Preferred_unit + value: milligram per liter + description: Measurement of the culture rooting medium micronutrients (Fe, Mn, + Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L) + title: rooting medium micronutrients + examples: + - value: H3BO3;6.2 milligram per liter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - micronutrients + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000579 + multivalued: false + required: false + recommended: false + root_med_ph: + name: root_med_ph + description: pH measurement of the culture rooting medium; e.g. 5.5 + title: rooting medium pH + examples: + - value: '7.5' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - ph + slot_uri: MIXS:0001062 + multivalued: false + range: float + required: false + recommended: false + root_med_regl: + name: root_med_regl + annotations: + Expected_value: + tag: Expected_value + value: regulator name;measurement value + Preferred_unit: + tag: Preferred_unit + value: milligram per liter + description: Growth regulators in the culture rooting medium such as cytokinins, + auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA + title: rooting medium regulators + examples: + - value: abscisic acid;0.75 milligram per liter + from_schema: https://w3id.org/mixs-6-2-rc + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000581 + multivalued: false + required: false + recommended: false + root_med_solid: + name: root_med_solid + description: Specification of the solidifying agent in the culture rooting medium; + e.g. agar + title: rooting medium solidifier + examples: + - value: agar + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0001063 + multivalued: false + range: string + required: false + recommended: false + root_med_suppl: + name: root_med_suppl + annotations: + Expected_value: + tag: Expected_value + value: supplement name;measurement value + Preferred_unit: + tag: Preferred_unit + value: milligram per liter + description: Organic supplements of the culture rooting medium, such as vitamins, + amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid + (0.5 mg/L) + title: rooting medium organic supplements + examples: + - value: nicotinic acid;0.5 milligram per liter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - organic + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000580 + multivalued: false + required: false + recommended: false + route_transmission: + name: route_transmission + description: Description of path taken by the symbiotic host organism being sampled + in order to establish a symbiotic relationship with the host (with which it + was observed at the time of sampling) via a mode of transmission (specified + in mode_transmission) + title: route of transmission + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - route + slot_uri: MIXS:0001316 + multivalued: false + range: ROUTE_TRANSMISSION_ENUM + required: false + recommended: false + salinity: + name: salinity + annotations: + Preferred_unit: + tag: Preferred_unit + value: practical salinity unit, percentage + description: The total concentration of all dissolved salts in a liquid or solid + sample. While salinity can be measured by a complete chemical analysis, this + method is difficult and time consuming. More often, it is instead derived from + the conductivity measurement. This is known as practical salinity. These derivations + compare the specific conductance of the sample to a salinity standard such as + seawater + title: salinity + examples: + - value: 25 practical salinity unit + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - salinity + slot_uri: MIXS:0000183 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + salt_regm: + name: salt_regm + annotations: + Preferred_unit: + tag: Preferred_unit + value: gram, microgram, mole per liter, gram per liter + description: Information about treatment involving use of salts as supplement + to liquid and soil growth media; should include the name of salt, amount administered, + treatment regimen including how many times the treatment was repeated, how long + each treatment lasted, and the start and end time of the entire treatment; can + include multiple salt regimens + title: salt regimen + examples: + - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - regimen + - salt + slot_uri: MIXS:0000582 + multivalued: true + range: string + samp_capt_status: + name: samp_capt_status + description: Reason for the sample + title: sample capture status + examples: + - value: farm sample + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + - status + slot_uri: MIXS:0000860 + multivalued: false + range: SAMP_CAPT_STATUS_ENUM + required: false + recommended: false + samp_collect_device: + name: samp_collect_device + annotations: + Expected_value: + tag: Expected_value + value: device name + description: The device used to collect an environmental sample. This field accepts + terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). + This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094) + title: sample collection device + in_subset: + - nucleic acid sequence source + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - device + - sample + string_serialization: '{termLabel} [{termID}]|{text}' + slot_uri: MIXS:0000002 + multivalued: false + samp_collect_method: + name: samp_collect_method + description: The method employed for collecting the sample + title: sample collection method + in_subset: + - nucleic acid sequence source + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - method + - sample + slot_uri: MIXS:0001225 + multivalued: false + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}|{text}$ + interpolated: true + partial_match: true + samp_collect_point: + name: samp_collect_point + description: Sampling point on the asset were sample was collected (e.g. Wellhead, + storage tank, separator, etc). If "other" is specified, please propose entry + in "additional info" field + title: sample collection point + examples: + - value: well + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + slot_uri: MIXS:0001015 + multivalued: false + range: SAMP_COLLECT_POINT_ENUM + required: true + samp_dis_stage: + name: samp_dis_stage + description: Stage of the disease at the time of sample collection, e.g. inoculation, + penetration, infection, growth and reproduction, dissemination of pathogen + title: sample disease stage + examples: + - value: infection + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - disease + - sample + slot_uri: MIXS:0000249 + multivalued: false + range: SAMP_DIS_STAGE_ENUM + required: false + recommended: false + samp_floor: + name: samp_floor + annotations: + Expected_value: + tag: Expected_value + value: enumeration + description: The floor of the building, where the sampling room is located + title: sampling floor + examples: + - value: 4th floor + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - floor + string_serialization: '[1st floor|2nd floor|{integer} floor|basement|lobby]' + slot_uri: MIXS:0000828 + multivalued: false + required: false + recommended: false + samp_loc_condition: + name: samp_loc_condition + description: The condition of the sample location at the time of sampling + title: sample location condition + examples: + - value: new + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - condition + - location + - sample + slot_uri: MIXS:0001257 + multivalued: false + range: SAMP_LOC_CONDITION_ENUM + required: false + recommended: false + samp_loc_corr_rate: + name: samp_loc_corr_rate + annotations: + Preferred_unit: + tag: Preferred_unit + value: millimeter per year + description: Metal corrosion rate is the speed of metal deterioration due to environmental + conditions. As environmental conditions change corrosion rates change accordingly. + Therefore, long term corrosion rates are generally more informative than short + term rates and for that reason they are preferred during reporting. In the case + of suspected MIC, corrosion rate measurements at the time of sampling might + provide insights into the involvement of certain microbial community members + in MIC as well as potential microbial interplays + title: corrosion rate at sample location + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - location + - rate + - sample + slot_uri: MIXS:0000136 + multivalued: false + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+ *- *[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{float} *- *{float} {unit}$ + interpolated: true + partial_match: true + samp_mat_process: + name: samp_mat_process + description: A brief description of any processing applied to the sample during + or after retrieving the sample from environment, or a link to the relevant protocol(s) + performed + title: sample material processing + examples: + - value: filtering of seawater, storing samples in ethanol + in_subset: + - nucleic acid sequence source + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - material + - process + - sample + slot_uri: MIXS:0000016 + multivalued: false + range: string + samp_md: + name: samp_md + annotations: + Expected_value: + tag: Expected_value + value: measurement value;enumeration + Preferred_unit: + tag: Preferred_unit + value: meter + description: In non deviated well, measured depth is equal to the true vertical + depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated + wells, the MD is the length of trajectory of the borehole measured from the + same reference or datum. Common datums used are ground level (GL), drilling + rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). + If "other" is specified, please propose entry in "additional info" field + title: sample measured depth + examples: + - value: 1534 meter;MSL + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - depth + - measurement + - sample + string_serialization: '{float} {unit};[GL|DF|RT|KB|MSL|other]' + slot_uri: MIXS:0000413 + multivalued: false + required: false + recommended: false + samp_name: + name: samp_name + annotations: + Preferred_unit: + tag: Preferred_unit + value: '' + description: A local identifier or name that for the material sample used for + extracting nucleic acids, and subsequent sequencing. It can refer either to + the original material collected or to any derived sub-samples. It can have any + format, but we suggest that you make it concise, unique and consistent within + your lab, and as informative as possible. INSDC requires every sample name from + a single Submitter to be unique. Use of a globally unique identifier for the + field source_mat_id is recommended in addition to sample_name + title: sample name + examples: + - value: ISDsoil1 + in_subset: + - investigation + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + slot_uri: MIXS:0001107 + multivalued: false + range: string + required: true + samp_pooling: + name: samp_pooling + description: Physical combination of several instances of like material, e.g. + RNA extracted from samples or dishes of cell cultures into one big aliquot of + cells. Please provide a short description of the samples that were pooled + title: sample pooling + examples: + - value: 5uL of extracted genomic DNA from 5 leaves were pooled + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - pooling + - sample + slot_uri: MIXS:0001153 + multivalued: true + range: string + samp_preserv: + name: samp_preserv + annotations: + Preferred_unit: + tag: Preferred_unit + value: milliliter + description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, + etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) + title: preservative added to sample + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + slot_uri: MIXS:0000463 + multivalued: false + range: string + required: false + recommended: false + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{name};{float} {unit}$ + interpolated: true + partial_match: true + samp_purpose: + name: samp_purpose + annotations: + Expected_value: + tag: Expected_value + value: enumeration or {text} + description: The reason that the sample was collected + title: purpose of sampling + examples: + - value: field trial + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - purpose + string_serialization: '[active surveillance in response to an outbreak|active + surveillance not initiated by an outbreak|clinical trial|cluster investigation|environmental + assessment|farm sample|field trial|for cause|industry internal investigation|market + sample|passive surveillance|population based studies|research|research and development] + or {text}' + slot_uri: MIXS:0001151 + multivalued: false + samp_rep_biol: + name: samp_rep_biol + description: Measurements of biologically distinct samples that show biological + variation + title: biological sample replicate + examples: + - value: 6 replicates + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + slot_uri: MIXS:0001226 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + samp_rep_tech: + name: samp_rep_tech + description: Repeated measurements of the same sample that show independent measures + of the noise associated with the equipment and the protocols + title: technical sample replicate + examples: + - value: 10 replicates + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + slot_uri: MIXS:0001227 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + samp_room_id: + name: samp_room_id + description: Sampling room number. This ID should be consistent with the designations + on the building floor plans + title: sampling room ID or name + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - identifier + - room + slot_uri: MIXS:0000244 + multivalued: false + range: integer + required: false + recommended: false + samp_size: + name: samp_size + description: The total amount or size (volume (ml), mass (g) or area (m2) ) of + sample collected + title: amount or size of sample collected + examples: + - value: 5 liter + in_subset: + - nucleic acid sequence source + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + - size + slot_uri: MIXS:0000001 + multivalued: false + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + samp_sort_meth: + name: samp_sort_meth + description: Method by which samples are sorted; open face filter collecting total + suspended particles, prefilter to remove particles larger than X micrometers + in diameter, where common values of X would be 10 and 2.5 full size sorting + in a cascade impactor + title: sample size sorting method + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - method + - sample + - size + slot_uri: MIXS:0000216 + multivalued: true + range: string + required: false + recommended: false + samp_source_mat_cat: + name: samp_source_mat_cat + annotations: + Expected_value: + tag: Expected_value + value: GENEPIO:0001237 + description: This is the scientific role or category that the subject organism + or material has with respect to an investigation. This field accepts terms + listed under specimen source material category (http://purl.obolibrary.org/obo/GENEPIO_0001237 + or http://purl.obolibrary.org/obo/OBI_0100051) + title: sample source material category + examples: + - value: environmental (swab or sampling) [GENEPIO:0001732] + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - material + - sample + - source + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0001154 + multivalued: false + samp_stor_device: + name: samp_stor_device + annotations: + Expected_value: + tag: Expected_value + value: NCIT:C4318 + description: The container used to store the sample. This field accepts terms + listed under container (http://purl.obolibrary.org/obo/NCIT_C43186). If the + proper descriptor is not listed please use text to describe the storage device + title: sample storage device + examples: + - value: Whirl Pak sampling bag [GENEPIO:0002122] + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - device + - sample + - storage + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001228 + multivalued: false + samp_stor_media: + name: samp_stor_media + description: The liquid that is added to the sample collection device prior to + sampling. If the sample is pre-hydrated, indicate the liquid media the sample + is pre-hydrated with for storage purposes. This field accepts terms listed under + microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067). + If the proper descriptor is not listed please use text to describe the sample + storage media + title: sample storage media + examples: + - value: peptone water medium [MICRO:0000548] + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + - storage + slot_uri: MIXS:0001229 + multivalued: false + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$ + structured_pattern: + syntax: ^{text}|({termLabel} \[{termID}\])$ + interpolated: true + partial_match: true + samp_store_dur: + name: samp_store_dur + description: Duration for which the sample was stored. Indicate the duration for + which the sample was stored written in ISO 8601 format + title: sample storage duration + examples: + - value: P1Y6M + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - duration + - period + - sample + - storage + slot_uri: MIXS:0000116 + multivalued: false + range: string + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true + samp_store_loc: + name: samp_store_loc + annotations: + Expected_value: + tag: Expected_value + value: location name + description: Location at which sample was stored, usually name of a specific freezer/room + title: sample storage location + examples: + - value: Freezer no:5 + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - location + - sample + - storage + string_serialization: '{text}' + slot_uri: MIXS:0000755 + multivalued: false + samp_store_sol: + name: samp_store_sol + annotations: + Expected_value: + tag: Expected_value + value: solution name + description: Solution within which sample was stored, if any + title: sample storage solution + examples: + - value: 5% ethanol + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + - storage + string_serialization: '{text}' + slot_uri: MIXS:0001317 + multivalued: false + required: false + recommended: false + samp_store_temp: + name: samp_store_temp + annotations: + Preferred_unit: + tag: Preferred_unit + value: degree Celsius + description: Temperature at which sample was stored, e.g. -80 degree Celsius + title: sample storage temperature + examples: + - value: -80 degree Celsius + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + - storage + - temperature + slot_uri: MIXS:0000110 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + samp_subtype: + name: samp_subtype + description: Name of sample sub-type. For example if "sample type" is "Produced + Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, + please propose entry in "additional info" field + title: sample subtype + examples: + - value: biofilm + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + slot_uri: MIXS:0000999 + multivalued: false + range: SAMP_SUBTYPE_ENUM + recommended: true + samp_surf_moisture: + name: samp_surf_moisture + description: Degree of water held on a sampled surface. If present, user can + state the degree of water held on surface (intermittent moisture, submerged). + If no surface moisture is present indicate not present + title: sample surface moisture + examples: + - value: submerged + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - moisture + - sample + - surface + slot_uri: MIXS:0001256 + multivalued: true + range: SAMP_SURF_MOISTURE_ENUM + required: false + recommended: false + samp_taxon_id: + name: samp_taxon_id + description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa + sample. Use 'synthetic metagenome for mock community/positive controls, or + 'blank sample' for negative controls + title: taxonomy ID of DNA sample + examples: + - value: Gut Metagenome [NCBITaxon:749906] + in_subset: + - investigation + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - dna + - identifier + - sample + - taxon + slot_uri: MIXS:0001320 + multivalued: false + range: string + required: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$ + structured_pattern: + syntax: ^{text} \[{NCBItaxon_id}\]$ + interpolated: true + partial_match: true + samp_time_out: + name: samp_time_out + annotations: + Expected_value: + tag: Expected_value + value: time + Preferred_unit: + tag: Preferred_unit + value: hour + description: The recent and long term history of outside sampling + title: sampling time outside + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - time + string_serialization: '{float}' + slot_uri: MIXS:0000196 + multivalued: false + required: false + recommended: false + samp_transport_cond: + name: samp_transport_cond + annotations: + Expected_value: + tag: Expected_value + value: measurement value;measurement value + Preferred_unit: + tag: Preferred_unit + value: days;degree Celsius + description: Sample transport duration (in days or hrs) and temperature the sample + was exposed to (e.g. 5.5 days; 20 C) + title: sample transport conditions + examples: + - value: 5 days;-20 degree Celsius + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - condition + - sample + - transport + string_serialization: '{float} {unit};{float} {unit}' + slot_uri: MIXS:0000410 + multivalued: false + required: false + recommended: false + samp_transport_cont: + name: samp_transport_cont + description: Conatiner in which the sample was stored during transport. Indicate + the location name + title: sample transport container + examples: + - value: cooler + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + - transport + slot_uri: MIXS:0001230 + multivalued: false + range: SAMP_TRANSPORT_CONT_ENUM + required: false + recommended: false + samp_transport_dur: + name: samp_transport_dur + annotations: + Preferred_unit: + tag: Preferred_unit + value: days + description: The duration of time from when the sample was collected until processed. + Indicate the duration for which the sample was stored written in ISO 8601 format + title: sample transport duration + examples: + - value: P10D + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - duration + - period + - sample + - transport + slot_uri: MIXS:0001231 + multivalued: false + range: string + required: false + recommended: false + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true + samp_transport_temp: + name: samp_transport_temp + annotations: + Expected_value: + tag: Expected_value + value: text or measurement value + Preferred_unit: + tag: Preferred_unit + value: degree Celsius + description: Temperature at which sample was transported, e.g. -20 or 4 degree + Celsius + title: sample transport temperature + examples: + - value: 4 degree Celsius + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + - temperature + - transport + string_serialization: '{float} {unit} {text}' + slot_uri: MIXS:0001232 + multivalued: false + required: false + recommended: false + samp_tvdss: + name: samp_tvdss + annotations: + Expected_value: + tag: Expected_value + value: measurement value or measurement value range + Preferred_unit: + tag: Preferred_unit + value: meter + description: Depth of the sample i.e. The vertical distance between the sea level + and the sampled position in the subsurface. Depth can be reported as an interval + for subsurface samples e.g. 1325.75-1362.25 m + title: sample true vertical depth subsea + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - depth + - sample + string_serialization: '{float}-{float} {unit}' + slot_uri: MIXS:0000409 + multivalued: false + recommended: true + samp_type: + name: samp_type + description: The type of material from which the sample was obtained. For the + Hydrocarbon package, samples include types like core, rock trimmings, drill + cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, + produced water, injected water, swabs, etc. For the Food Package, samples are + usually categorized as food, body products or tissues, or environmental material. + This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246) + title: sample type + examples: + - value: built environment sample [GENEPIO:0001248] + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + - type + slot_uri: MIXS:0000998 + multivalued: false + range: string + required: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + annotations: + Preferred_unit: + tag: Preferred_unit + value: milliliter, gram, milligram, square centimeter + description: 'Volume (ml) or mass (g) of total collected sample processed for + DNA extraction. Note: total sample collected should be entered under the term + Sample Size (MIXS:0000001)' + title: sample volume or weight for DNA extraction + examples: + - value: 1500 milliliter + in_subset: + - nucleic acid sequence source + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - dna + - sample + - volume + - weight + slot_uri: MIXS:0000111 + multivalued: false + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + samp_weather: + name: samp_weather + description: The weather on the sampling day + title: sampling day weather + examples: + - value: foggy + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - day + - weather + slot_uri: MIXS:0000827 + multivalued: false + range: SAMP_WEATHER_ENUM + required: false + recommended: false + samp_well_name: + name: samp_well_name + description: Name of the well (e.g. BXA1123) where sample was taken + title: sample well name + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sample + slot_uri: MIXS:0000296 + multivalued: false + range: string + recommended: true + saturates_pc: + name: saturates_pc + annotations: + Preferred_unit: + tag: Preferred_unit + value: percent + description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis + method that divides crude oil components according to their polarizability + and polarity. There are three main methods to obtain SARA results. The most + popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: + https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' + title: saturates wt% + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000131 + multivalued: false + range: string + recommended: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{name};{float} {unit}$ + interpolated: true + partial_match: true + sc_lysis_approach: + name: sc_lysis_approach + description: Method used to free DNA from interior of the cell(s) or particle(s) + title: single cell or viral particle lysis approach + examples: + - value: enzymatic + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - particle + - single + slot_uri: MIXS:0000076 + multivalued: false + range: SC_LYSIS_APPROACH_ENUM + sc_lysis_method: + name: sc_lysis_method + annotations: + Expected_value: + tag: Expected_value + value: kit, protocol name + description: Name of the kit or standard protocol used for cell(s) or particle(s) + lysis + title: single cell or viral particle lysis kit protocol + examples: + - value: ambion single cell lysis kit + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - kit + - particle + - protocol + - single + string_serialization: '{text}' + slot_uri: MIXS:0000054 + multivalued: false + season: + name: season + annotations: + Expected_value: + tag: Expected_value + value: autumn [NCIT:C94733], spring [NCIT:C94731], summer [NCIT:C94732], winter + [NCIT:C94730] + description: The season when sampling occurred. Any of the four periods into which + the year is divided by the equinoxes and solstices. This field accepts terms + listed under season (http://purl.obolibrary.org/obo/NCIT_C94729) + title: season + comments: + - autumn [NCIT:C94733] does not match ^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$ + - would require ^\\S+.*\\S+ \\[[a-zA-Z]{2,}:[a-zA-Z0-9]\\]$ + examples: + - value: autumn [NCIT:C94733] + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - season + string_serialization: '{termLabel} [{termID}]' + slot_uri: MIXS:0000829 + range: string + required: false + recommended: false + pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:[a-zA-Z0-9]+\]$ + season_environment: + name: season_environment + description: Treatment involving an exposure to a particular season (e.g. Winter, + summer, rabi, rainy etc.), treatment regimen including how many times the treatment + was repeated, how long each treatment lasted, and the start and end time of + the entire treatment + title: seasonal environment + examples: + - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - environment + - season + slot_uri: MIXS:0001068 + multivalued: true + range: string + season_humidity: + name: season_humidity + description: Average humidity of the region throughout the growing season + title: mean seasonal humidity + comments: + - percent or float? + examples: + - value: '0.25' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - humidity + - mean + - season + slot_uri: MIXS:0001148 + range: float + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + season_precpt: + name: season_precpt + annotations: + Preferred_unit: + tag: Preferred_unit + value: millimeter + description: The average of all seasonal precipitation values known, or an estimated + equivalent value derived by such methods as regional indexes or Isohyetal maps + title: mean seasonal precipitation + examples: + - value: 75 millimeters + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - mean + - season + slot_uri: MIXS:0000645 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + season_temp: + name: season_temp + annotations: + Preferred_unit: + tag: Preferred_unit + value: degree Celsius + description: Mean seasonal temperature + title: mean seasonal temperature + examples: + - value: 18 degree Celsius + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - mean + - season + - temperature + slot_uri: MIXS:0000643 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + season_use: + name: season_use + description: The seasons the space is occupied + title: seasonal use + examples: + - value: Winter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - season + - use + slot_uri: MIXS:0000830 + multivalued: false + range: SEASON_USE_ENUM + required: false + recommended: false + secondary_treatment: + name: secondary_treatment + annotations: + Expected_value: + tag: Expected_value + value: secondary treatment type + description: The process for substantially degrading the biological content of + the sewage + title: secondary treatment + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - secondary + - treatment + string_serialization: '{text}' + slot_uri: MIXS:0000351 + multivalued: false + required: false + recommended: false + sediment_type: + name: sediment_type + description: Information about the sediment type based on major constituents + title: sediment type + examples: + - value: biogenous + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sediment + - type + slot_uri: MIXS:0001078 + multivalued: false + range: SEDIMENT_TYPE_ENUM + required: false + recommended: false + seq_meth: + name: seq_meth + description: Sequencing machine used. Where possible the term should be taken + from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103) + title: sequencing method + examples: + - value: 454 Genome Sequencer FLX [OBI:0000702] + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - method + slot_uri: MIXS:0000050 + multivalued: false + range: string + required: true + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$ + structured_pattern: + syntax: ^{text}|({termLabel} \[{termID}\])$ + interpolated: true + partial_match: true + seq_quality_check: + name: seq_quality_check + annotations: + Expected_value: + tag: Expected_value + value: none or manually edited + description: Indicate if the sequence has been called by automatic systems (none) + or undergone a manual editing procedure (e.g. by inspecting the raw data or + chromatograms). Applied only for sequences that are not submitted to SRA,ENA + or DRA + title: sequence quality check + examples: + - value: none + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - quality + slot_uri: MIXS:0000051 + multivalued: false + range: SEQ_QUALITY_CHECK_ENUM + sequencing_kit: + name: sequencing_kit + annotations: + Expected_value: + tag: Expected_value + value: name of sequencing kit used + description: Pre-filled, ready-to-use reagent cartridges. Used to produce improved + chemistry, cluster density and read length as well as improve quality (Q) scores. + Reagent components are encoded to interact with the sequencing system to validate + compatibility with user-defined applications. Indicate name of the sequencing + kit + title: sequencing kit + examples: + - value: NextSeq 500/550 High Output Kit v2.5 (75 Cycles) + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - kit + string_serialization: '{text}' + slot_uri: MIXS:0001155 + multivalued: false + required: false + recommended: false + sequencing_location: + name: sequencing_location + description: The location the sequencing run was performed. Indicate the name + of the lab or core facility where samples were sequenced + title: sequencing location + examples: + - value: University of Maryland Genomics Resource Center + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - location + slot_uri: MIXS:0001156 + multivalued: false + range: string + required: false + recommended: false + serovar_or_serotype: + name: serovar_or_serotype + description: A characterization of a cell or microorganism based on the antigenic + properties of the molecules on its surface. Indicate the name of a serovar or + serotype of interest. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). + This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy + title: serovar or serotype + examples: + - value: Escherichia coli strain O157:H7 [NCIT:C86883] + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0001157 + multivalued: true + range: string + required: false + recommended: false + pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ + structured_pattern: + syntax: ^({termLabel} \[{termID}\])|{integer}$ + interpolated: true + partial_match: true + sewage_type: + name: sewage_type + annotations: + Expected_value: + tag: Expected_value + value: sewage type name + description: Type of wastewater treatment plant as municipial or industrial + title: sewage type + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - type + string_serialization: '{text}' + slot_uri: MIXS:0000215 + multivalued: false + required: false + recommended: false + sexual_act: + name: sexual_act + annotations: + Expected_value: + tag: Expected_value + value: partner sex;frequency + description: Current sexual partner and frequency of sex + title: sexual activity + from_schema: https://w3id.org/mixs-6-2-rc + string_serialization: '{text}' + slot_uri: MIXS:0000285 + multivalued: false + required: false + recommended: false + shad_dev_water_mold: + name: shad_dev_water_mold + description: Signs of the presence of mold or mildew on the shading device + title: shading device signs of water/mold + examples: + - value: no presence of mold visible + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - device + slot_uri: MIXS:0000834 + multivalued: false + range: SHARED_ENUM_1 + required: false + recommended: false + shading_device_cond: + name: shading_device_cond + description: The physical condition of the shading device at the time of sampling + title: shading device condition + examples: + - value: new + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - condition + - device + slot_uri: MIXS:0000831 + multivalued: false + range: SHARED_ENUM_2 + required: false + recommended: false + shading_device_loc: + name: shading_device_loc + description: The location of the shading device in relation to the built structure + title: shading device location + examples: + - value: exterior + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - device + - location + slot_uri: MIXS:0000832 + multivalued: false + range: SHADING_DEVICE_LOC_ENUM + required: false + recommended: false + shading_device_mat: + name: shading_device_mat + annotations: + Expected_value: + tag: Expected_value + value: material name + description: The material the shading device is composed of + title: shading device material + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - device + - material + string_serialization: '{text}' + slot_uri: MIXS:0000245 + multivalued: false + required: false + recommended: false + shading_device_type: + name: shading_device_type + description: The type of shading device + title: shading device type + examples: + - value: slatted aluminum + description: was slatted aluminum awning + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - device + - type + slot_uri: MIXS:0000835 + range: SHADING_DEVICE_TYPE_ENUM + required: false + recommended: false + sieving: + name: sieving + annotations: + Expected_value: + tag: Expected_value + value: design name and/or size;amount + description: Collection design of pooled samples and/or sieve size and amount + of sample sieved + title: sieving + from_schema: https://w3id.org/mixs-6-2-rc + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000322 + multivalued: false + silicate: + name: silicate + annotations: + Preferred_unit: + tag: Preferred_unit + value: micromole per liter + description: Concentration of silicate + title: silicate + examples: + - value: 0.05 micromole per liter + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000184 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + sim_search_meth: + name: sim_search_meth + description: Tool used to compare ORFs with database, along with version and cutoffs + used + title: similarity search method + examples: + - value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - method + slot_uri: MIXS:0000063 + multivalued: false + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{software};{version};{parameters}$ + interpolated: true + partial_match: true + size_frac: + name: size_frac + annotations: + Expected_value: + tag: Expected_value + value: filter size value range + description: Filtering pore size used in sample preparation + title: size fraction selected + examples: + - value: 0-0.22 micrometer + in_subset: + - nucleic acid sequence source + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - fraction + - size + string_serialization: '{float}-{float} {unit}' + slot_uri: MIXS:0000017 + multivalued: false + size_frac_low: + name: size_frac_low + annotations: + Preferred_unit: + tag: Preferred_unit + value: micrometer + description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. + Materials larger than the size threshold are excluded from the sample + title: size-fraction lower threshold + examples: + - value: 0.2 micrometer + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - lower + slot_uri: MIXS:0000735 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + size_frac_up: + name: size_frac_up + annotations: + Preferred_unit: + tag: Preferred_unit + value: micrometer + description: Mesh or pore size of the device used to retain the sample. Materials + smaller than the size threshold are excluded from the sample + title: size-fraction upper threshold + examples: + - value: 20 micrometer + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - upper + slot_uri: MIXS:0000736 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + slope_aspect: + name: slope_aspect + annotations: + Preferred_unit: + tag: Preferred_unit + value: degree + description: The direction a slope faces. While looking down a slope use a compass + to record the direction you are facing (direction or degrees); e.g., nw or 315 + degrees. This measure provides an indication of sun and wind exposure that will + influence soil temperature and evapotranspiration + title: slope aspect + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - slope + slot_uri: MIXS:0000647 + multivalued: false + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + slope_gradient: + name: slope_gradient + annotations: + Preferred_unit: + tag: Preferred_unit + value: percentage + description: Commonly called 'slope'. The angle between ground surface and a horizontal + line (in percent). This is the direction that overland water would flow. This + measure is usually taken with a hand level meter or clinometer + title: slope gradient + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - slope + slot_uri: MIXS:0000646 + multivalued: false + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + sludge_retent_time: + name: sludge_retent_time + annotations: + Preferred_unit: + tag: Preferred_unit + value: hours + description: The time activated sludge remains in reactor + title: sludge retention time + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - time + slot_uri: MIXS:0000669 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + smoker: + name: smoker + description: Specification of smoking status + title: smoker + examples: + - value: 'yes' + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000262 + multivalued: false + range: boolean + required: false + recommended: false + sodium: + name: sodium + annotations: + Preferred_unit: + tag: Preferred_unit + value: milligram per liter, parts per million + description: Sodium concentration in the sample + title: sodium + examples: + - value: 10.5 milligram per liter + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000428 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + soil_conductivity: + name: soil_conductivity + annotations: + Preferred_unit: + tag: Preferred_unit + value: milliSiemens per centimeter + title: soil conductivity + examples: + - value: 10 milliSiemens per centimeter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - soil + slot_uri: MIXS:0001158 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + soil_cover: + name: soil_cover + annotations: + Expected_value: + tag: Expected_value + value: subclass of 'environmental material', http://purl.obolibrary.org/obo/ENVO_00010483 + description: Material covering the sampled soil. This field accepts terms under + ENVO:00010483, environmental material + title: soil cover + examples: + - value: bare soil [ENVO01001616] + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - soil + string_serialization: bare soil [ENVO:01001616] + slot_uri: MIXS:0001159 + multivalued: false + soil_horizon: + name: soil_horizon + description: Specific layer in the land area which measures parallel to the soil + surface and possesses physical characteristics which differ from the layers + above and beneath + title: soil horizon + examples: + - value: A horizon + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - horizon + - soil + slot_uri: MIXS:0001082 + multivalued: false + range: SOIL_HORIZON_ENUM + soil_pH: + name: soil_pH + title: soil pH + examples: + - value: '7.2' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - ph + - soil + slot_uri: MIXS:0001160 + range: float + required: false + recommended: false + soil_porosity: + name: soil_porosity + annotations: + Expected_value: + tag: Expected_value + value: percent porosity + Preferred_unit: + tag: Preferred_unit + value: percentage + description: Porosity of soil or deposited sediment is volume of voids divided + by the total volume of sample + title: soil sediment porosity + examples: + - value: '0.2' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - porosity + - sediment + - soil + string_serialization: '{percentage}' + slot_uri: MIXS:0001162 + multivalued: false + required: false + recommended: false + soil_temp: + name: soil_temp + annotations: + Preferred_unit: + tag: Preferred_unit + value: degree Celsius + description: Temperature of soil at the time of sampling + title: soil temperature + examples: + - value: 25 degrees Celsius + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - soil + - temperature + slot_uri: MIXS:0001163 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + soil_texture: + name: soil_texture + description: The relative proportion of different grain sizes of mineral particles + in a soil, as described using a standard system; express as % sand (50 um to + 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty + clay loam) optional + title: soil texture + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - soil + - texture + slot_uri: MIXS:0000335 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + soil_texture_class: + name: soil_texture_class + description: One of the 12 soil texture classes use to describe soil texture based + on the relative proportion of different grain sizes of mineral particles [sand + (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um)] in a soil + title: soil texture classification + examples: + - value: silty clay loam + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - classification + - soil + - texture + slot_uri: MIXS:0001164 + multivalued: false + range: SOIL_TEXTURE_CLASS_ENUM + required: false + recommended: false + soil_texture_meth: + name: soil_texture_meth + description: Reference or method used in determining soil texture + title: soil texture method + examples: + - value: https://uwlab.soils.wisc.edu/wp-content/uploads/sites/17/2015/09/particle_size.pdf + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - method + - soil + - texture + slot_uri: MIXS:0000336 + multivalued: false + range: string + required: false + recommended: false + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + soil_type: + name: soil_type + annotations: + Expected_value: + tag: Expected_value + value: ENVO:00001998 + description: Description of the soil type or classification. This field accepts + terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms + can be separated by pipes + title: soil type + examples: + - value: plinthosol [ENVO:00002250] + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - soil + - type + slot_uri: MIXS:0000332 + multivalued: false + soil_type_meth: + name: soil_type_meth + description: Reference or method used in determining soil series name or other + lower-level classification + title: soil type method + examples: + - value: https://www.lrh.usace.army.mil/Portals/38/docs/PR/BluestoneSFEIS/Appendix%20K-Soil%20Descriptions.pdf + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - method + - soil + - type + slot_uri: MIXS:0000334 + multivalued: false + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + solar_irradiance: + name: solar_irradiance + annotations: + Preferred_unit: + tag: Preferred_unit + value: kilowatts per square meter per day, ergs per square centimeter per + second + description: The amount of solar energy that arrives at a specific area of a surface + during a specific time interval + title: solar irradiance + examples: + - value: 1.36 kilowatts per square meter per day + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000112 + multivalued: true + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + soluble_inorg_mat: + name: soluble_inorg_mat + annotations: + Expected_value: + tag: Expected_value + value: soluble inorganic material name;measurement value + Preferred_unit: + tag: Preferred_unit + value: gram, microgram, mole per liter, gram per liter, parts per million + description: Concentration of substances such as ammonia, road-salt, sea-salt, + cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc + title: soluble inorganic material + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - inorganic + - material + - soluble + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000672 + multivalued: true + required: false + recommended: false + soluble_org_mat: + name: soluble_org_mat + annotations: + Expected_value: + tag: Expected_value + value: soluble organic material name;measurement value + Preferred_unit: + tag: Preferred_unit + value: gram, microgram, mole per liter, gram per liter, parts per million + description: Concentration of substances such as urea, fruit sugars, soluble proteins, + drugs, pharmaceuticals, etc + title: soluble organic material + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - material + - organic + - soluble + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000673 + multivalued: true + required: false + recommended: false + soluble_react_phosp: + name: soluble_react_phosp + annotations: + Preferred_unit: + tag: Preferred_unit + value: micromole per liter, milligram per liter, parts per million + description: Concentration of soluble reactive phosphorus + title: soluble reactive phosphorus + examples: + - value: 0.1 milligram per liter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - phosphorus + - soluble + slot_uri: MIXS:0000738 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + sop: + name: sop + annotations: + Expected_value: + tag: Expected_value + value: reference to SOP + description: Standard operating procedures used in assembly and/or annotation + of genomes, metagenomes or environmental sequences + title: relevant standard operating procedures + examples: + - value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/ + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - procedures + string_serialization: '{PMID}|{DOI}|{URL}' + slot_uri: MIXS:0000090 + multivalued: true + sort_tech: + name: sort_tech + description: Method used to sort/isolate cells or particles of interest + title: sorting technology + examples: + - value: optical manipulation + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000075 + multivalued: false + range: SORT_TECH_ENUM + source_mat_id: + name: source_mat_id + annotations: + Expected_value: + tag: Expected_value + value: 'for cultures of microorganisms: identifiers for two culture collections; + for other material a unique arbitrary identifer' + description: A unique identifier assigned to a material sample (as defined by + http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular + digital record of a material sample) used for extracting nucleic acids, and + subsequent sequencing. The identifier can refer either to the original material + collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, + /bio_material, or /culture_collection may or may not share the same value as + the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id + may both contain 'UAM:Herps:14' , referring to both the specimen voucher and + sampled tissue with the same identifier. However, the /culture_collection qualifier + may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id + would refer to an identifier from some derived culture from which the nucleic + acids were extracted (e.g. xatc123 or ark:/2154/R2) + title: source material identifiers + examples: + - value: MPI012345 + in_subset: + - nucleic acid sequence source + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - identifier + - material + - source + string_serialization: '{text}' + slot_uri: MIXS:0000026 + multivalued: true + source_uvig: + name: source_uvig + annotations: + Expected_value: + tag: Expected_value + value: enumeration + description: Type of dataset from which the UViG was obtained + title: source of UViGs + examples: + - value: viral fraction metagenome (virome) + in_subset: + - nucleic acid sequence source + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - source + string_serialization: '[metagenome (not viral targeted)|viral fraction metagenome + (virome)|sequence-targeted metagenome|metatranscriptome (not viral targeted)|viral + fraction RNA metagenome (RNA virome)|sequence-targeted RNA metagenome|microbial + single amplified genome (SAG)|viral single amplified genome (vSAG)|isolate microbial + genome|other]' + slot_uri: MIXS:0000035 + multivalued: false + space_typ_state: + name: space_typ_state + description: Customary or normal state of the space + title: space typical state + examples: + - value: typically occupied + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000770 + multivalued: false + range: SPACE_TYP_STATE_ENUM + required: true + spec_intended_cons: + name: spec_intended_cons + description: Food consumer type, human or animal, for which the food product is + produced and marketed. This field accepts terms listed under food consumer group + (http://purl.obolibrary.org/obo/FOODON_03510136) + title: specific intended consumer + examples: + - value: senior as food consumer [FOODON:03510254] + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - consumer + slot_uri: MIXS:0001234 + multivalued: true + range: string + required: false + recommended: false + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$ + structured_pattern: + syntax: ^{termLabel} \[{termID}\]$ + interpolated: true + partial_match: true + special_diet: + name: special_diet + annotations: + Expected_value: + tag: Expected_value + value: enumeration + description: Specification of special diet; can include multiple special diets + title: special diet + examples: + - value: other:vegan + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - diet + string_serialization: '[low carb|reduced calorie|vegetarian|other(to be specified)]' + slot_uri: MIXS:0000905 + multivalued: true + required: false + recommended: false + specific: + name: specific + description: 'The building specifications. If design is chosen, indicate phase: + conceptual, schematic, design development, construction documents' + title: specifications + examples: + - value: construction + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000836 + multivalued: false + range: SPECIFIC_ENUM + required: false + recommended: false + specific_host: + name: specific_host + annotations: + Expected_value: + tag: Expected_value + value: host scientific name, taxonomy ID + description: Report the host's taxonomic name and/or NCBI taxonomy ID + title: host scientific name + examples: + - value: Homo sapiens and/or 9606 + in_subset: + - nucleic acid sequence source + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - host + - host. + string_serialization: '{text}|{NCBI taxid}' + slot_uri: MIXS:0000029 + multivalued: false + specific_humidity: + name: specific_humidity + annotations: + Preferred_unit: + tag: Preferred_unit + value: gram of air, kilogram of air + description: The mass of water vapour in a unit mass of moist air, usually expressed + as grams of vapour per kilogram of air, or, in air conditioning, as grains per + pound + title: specific humidity + examples: + - value: 15 per kilogram of air + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - humidity + slot_uri: MIXS:0000214 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + spikein_AMR: + name: spikein_AMR + annotations: + Expected_value: + tag: Expected_value + value: measurement value ARO:3004299 + description: Qualitative description of a microbial response to antimicrobial + agents. Bacteria may be susceptible or resistant to a broad range of antibiotic + drugs or drug classes, with several intermediate states or phases. This field + accepts terms under antimicrobial phenotype (http://purl.obolibrary.org/obo/ARO_3004299) + title: antimicrobial phenotype of spike-in bacteria + examples: + - value: wild type [ARO:3004432] + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - antimicrobial + - spike + string_serialization: '{float} {unit};{termLabel} [{termID}]' + slot_uri: MIXS:0001235 + multivalued: true + required: false + recommended: false + spikein_antibiotic: + name: spikein_antibiotic + annotations: + Expected_value: + tag: Expected_value + value: drug name; concentration + description: Antimicrobials used in research study to assess effects of exposure + on microbiome of a specific site. Please list antimicrobial, common name and/or + class and concentration used for spike-in + title: spike-in with antibiotics + examples: + - value: Tetracycline at 5 mg/ml + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - spike + string_serialization: '{text} {integer}' + slot_uri: MIXS:0001171 + multivalued: true + required: false + recommended: false + spikein_count: + name: spikein_count + annotations: + Expected_value: + tag: Expected_value + value: organism name;measurement value;enumeration + Preferred_unit: + tag: Preferred_unit + value: colony forming units per milliliter; colony forming units per gram + of dry weight + description: 'Total cell count of any organism (or group of organisms) per gram, + volume or area of sample, should include name of organism followed by count. + The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) should + also be provided (example: total prokaryotes; 3.5e7 cells per ml; qPCR)' + title: spike-in organism count + examples: + - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - count + - organism + - spike + string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]' + slot_uri: MIXS:0001335 + multivalued: false + required: false + recommended: false + spikein_growth_med: + name: spikein_growth_med + description: A liquid or gel containing nutrients, salts, and other factors formulated + to support the growth of microorganisms, cells, or plants (National Cancer Institute + Thesaurus). A growth medium is a culture medium which has the disposition to + encourage growth of particular bacteria to the exclusion of others in the same + growth environment. In this case, list the culture medium used to propagate + the spike-in bacteria during preparation of spike-in inoculum. This field accepts + terms listed under microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067). + If the proper descriptor is not listed please use text to describe the spike + in growth media + title: spike-in growth medium + examples: + - value: LB broth [MCO:0000036] + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - growth + - spike + slot_uri: MIXS:0001169 + multivalued: true + range: string + required: false + recommended: false + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$ + structured_pattern: + syntax: ^{text}|({termLabel} \[{termID}\])$ + interpolated: true + partial_match: true + spikein_metal: + name: spikein_metal + annotations: + Expected_value: + tag: Expected_value + value: heavy metal name or chemical symbol; concentration + description: Heavy metals used in research study to assess effects of exposure + on microbiome of a specific site. Please list heavy metals and concentration + used for spike-in + title: spike-in with heavy metals + examples: + - value: Cd at 20 ppm + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - heavy + - spike + string_serialization: '{text} {integer}' + slot_uri: MIXS:0001172 + multivalued: true + required: false + recommended: false + spikein_org: + name: spikein_org + description: Taxonomic information about the spike-in organism(s). This field + accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This + field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. + Multiple terms can be separated by pipes + title: spike in organism + examples: + - value: Listeria monocytogenes [NCIT:C86502]|28901 + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - organism + - spike + slot_uri: MIXS:0001167 + multivalued: true + range: string + required: false + recommended: false + pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$ + structured_pattern: + syntax: ^({termLabel} \[{termID}\])|{integer}$ + interpolated: true + partial_match: true + spikein_serovar: + name: spikein_serovar + annotations: + Expected_value: + tag: Expected_value + value: NCIT:C14250 or antigenic formula or serovar name + description: Taxonomic information about the spike-in organism(s) at the serovar + or serotype level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). + This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. + Multiple terms can be separated by pipes + title: spike-in bacterial serovar or serotype + examples: + - value: Escherichia coli strain O157:H7 [NCIT:C86883]|83334 + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - spike + string_serialization: '{termLabel} [{termID}]|{integer}' + slot_uri: MIXS:0001168 + multivalued: true + required: false + recommended: false + spikein_strain: + name: spikein_strain + annotations: + Expected_value: + tag: Expected_value + value: NCIT:C14250 or NCBI taxid or text + description: Taxonomic information about the spike-in organism(s) at the strain + level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). + This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. + Multiple terms can be separated by pipes + title: spike-in microbial strain + examples: + - value: '169963' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - microbial + - spike + string_serialization: '{termLabel} [{termID}]|{integer}' + slot_uri: MIXS:0001170 + multivalued: true + required: false + recommended: false + sr_dep_env: + name: sr_dep_env + description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). + If "other" is specified, please propose entry in "additional info" field + title: source rock depositional environment + examples: + - value: Marine + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - environment + - source + slot_uri: MIXS:0000996 + multivalued: false + range: SR_DEP_ENV_ENUM + required: false + recommended: false + sr_geol_age: + name: sr_geol_age + description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). + If "other" is specified, please propose entry in "additional info" field' + title: source rock geological age + examples: + - value: Silurian + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - age + - source + slot_uri: MIXS:0000997 + multivalued: false + range: SHARED_ENUM_5 + required: false + recommended: false + sr_kerog_type: + name: sr_kerog_type + description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic + and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ + fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris + (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). + If "other" is specified, please propose entry in "additional info" field' + title: source rock kerogen type + examples: + - value: Type IV + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - source + - type + slot_uri: MIXS:0000994 + multivalued: false + range: SR_KEROG_TYPE_ENUM + required: false + recommended: false + sr_lithology: + name: sr_lithology + description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). + If "other" is specified, please propose entry in "additional info" field + title: source rock lithology + examples: + - value: Coal + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - lithology + - source + slot_uri: MIXS:0000995 + multivalued: false + range: SR_LITHOLOGY_ENUM + required: false + recommended: false + standing_water_regm: + name: standing_water_regm + description: Treatment involving an exposure to standing water during a plant's + life span, types can be flood water or standing water, treatment regimen including + how many times the treatment was repeated, how long each treatment lasted, and + the start and end time of the entire treatment; can include multiple regimens + title: standing water regimen + examples: + - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - regimen + - water + slot_uri: MIXS:0001069 + multivalued: true + range: string + ster_meth_samp_room: + name: ster_meth_samp_room + annotations: + Expected_value: + tag: Expected_value + value: ENVO:01001026 + description: The method used to sterilize the sampling room. This field accepts + terms listed under electromagnetic radiation (http://purl.obolibrary.org/obo/ENVO_01001026). + If the proper descriptor is not listed, please use text to describe the sampling + room sterilization method. Multiple terms can be separated by pipes + title: sampling room sterilization method + examples: + - value: ultraviolet radiation [ENVO:21001216]|infrared radiation [ENVO:21001214] + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - method + - room + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001259 + multivalued: true + required: false + recommended: false + store_cond: + name: store_cond + annotations: + Expected_value: + tag: Expected_value + value: storage condition type;duration + description: Explain how and for how long the soil sample was stored before DNA + extraction (fresh/frozen/other) + title: storage conditions + examples: + - value: -20 degree Celsius freezer;P2Y10D + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - condition + - storage + string_serialization: '{text};{period}' + slot_uri: MIXS:0000327 + multivalued: false + study_complt_stat: + name: study_complt_stat + annotations: + Expected_value: + tag: Expected_value + value: YES or NO due to (1)adverse event (2) non-compliance (3) lost to follow + up (4)other-specify + description: Specification of study completion status, if no the reason should + be specified + title: study completion status + examples: + - value: no;non-compliance + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - status + string_serialization: '{boolean};[adverse event|non-compliance|lost to follow + up|other-specify]' + slot_uri: MIXS:0000898 + multivalued: false + required: false + recommended: false + study_design: + name: study_design + annotations: + Expected_value: + tag: Expected_value + value: OBI:0500000 + description: A plan specification comprised of protocols (which may specify how + and what kinds of data will be gathered) that are executed as part of an investigation + and is realized during a study design execution. This field accepts terms under + study design (http://purl.obolibrary.org/obo/OBI_0500000). If the proper descriptor + is not listed please use text to describe the study design. Multiple terms can + be separated by pipes + title: study design + examples: + - value: in vitro design [OBI:0001285] + from_schema: https://w3id.org/mixs-6-2-rc + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001236 + multivalued: true + required: false + recommended: false + study_inc_dur: + name: study_inc_dur + annotations: + Preferred_unit: + tag: Preferred_unit + value: hours or days + description: Sample incubation duration if unpublished or unvalidated method is + used. Indicate the timepoint written in ISO 8601 format + title: study incubation duration + examples: + - value: PT24H + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - duration + - incubation + - period + slot_uri: MIXS:0001237 + multivalued: false + range: string + required: false + recommended: false + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true + study_inc_temp: + name: study_inc_temp + annotations: + Preferred_unit: + tag: Preferred_unit + value: degree Celsius + description: Sample incubation temperature if unpublished or unvalidated method + is used + title: study incubation temperature + examples: + - value: 37 degree Celsius + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - incubation + - temperature + slot_uri: MIXS:0001238 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + study_timecourse: + name: study_timecourse + annotations: + Preferred_unit: + tag: Preferred_unit + value: dpi + description: For time-course research studies involving samples of the food commodity, + indicate the total duration of the time-course study + title: time-course duration + examples: + - value: 2 days post inoculation + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - duration + - period + - time + slot_uri: MIXS:0001239 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + study_tmnt: + name: study_tmnt + annotations: + Expected_value: + tag: Expected_value + value: MCO:0000866 + description: A process in which the act is intended to modify or alter some other + material entity. From the study design, each treatment is comprised of one + level of one or multiple factors. This field accepts terms listed under treatment + (http://purl.obolibrary.org/obo/MCO_0000866). If the proper descriptor is not + listed please use text to describe the study treatment. Multiple terms can be + separated by one or more pipes + title: study treatment + examples: + - value: Factor A|spike-in|levels high, medium, low + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - treatment + string_serialization: '{text}|{termLabel} [{termID}]' + slot_uri: MIXS:0001240 + multivalued: true + required: false + recommended: false + subspecf_gen_lin: + name: subspecf_gen_lin + annotations: + Expected_value: + tag: Expected_value + value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, + e.g. serovar, biotype, ecotype, variety, cultivar + description: Information about the genetic distinctness of the sequenced organism + below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any + relevant genetic typing schemes like Group I plasmid. Subspecies should not + be recorded in this term, but in the NCBI taxonomy. Supply both the lineage + name and the lineage rank separated by a colon, e.g., biovar:abc123 + title: subspecific genetic lineage + examples: + - value: serovar:Newport + in_subset: + - nucleic acid sequence source + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - lineage + string_serialization: '{rank name}:{text}' + slot_uri: MIXS:0000020 + multivalued: false + substructure_type: + name: substructure_type + description: The substructure or under building is that largely hidden section + of the building which is built off the foundations to the ground floor level + title: substructure type + examples: + - value: basement + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - type + slot_uri: MIXS:0000767 + multivalued: true + range: SUBSTRUCTURE_TYPE_ENUM + required: false + recommended: false + sulfate: + name: sulfate + annotations: + Preferred_unit: + tag: Preferred_unit + value: micromole per liter, milligram per liter, parts per million + description: Concentration of sulfate in the sample + title: sulfate + examples: + - value: 5 micromole per liter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sulfate + slot_uri: MIXS:0000423 + multivalued: false + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + sulfate_fw: + name: sulfate_fw + annotations: + Preferred_unit: + tag: Preferred_unit + value: milligram per liter + description: Original sulfate concentration in the hydrocarbon resource + title: sulfate in formation water + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sulfate + - water + slot_uri: MIXS:0000407 + multivalued: false + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + sulfide: + name: sulfide + annotations: + Preferred_unit: + tag: Preferred_unit + value: micromole per liter, milligram per liter, parts per million + description: Concentration of sulfide in the sample + title: sulfide + examples: + - value: 2 micromole per liter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sulfide + slot_uri: MIXS:0000424 + multivalued: false + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + surf_air_cont: + name: surf_air_cont + description: Contaminant identified on surface + title: surface-air contaminant + examples: + - value: radon + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000759 + multivalued: true + range: SURF_AIR_CONT_ENUM + recommended: true + surf_humidity: + name: surf_humidity + annotations: + Preferred_unit: + tag: Preferred_unit + value: percentage + description: 'Surfaces: water activity as a function of air and material moisture' + title: surface humidity + comments: + - percent or float? + examples: + - value: '0.1' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - humidity + - surface + slot_uri: MIXS:0000123 + range: float + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + surf_material: + name: surf_material + description: Surface materials at the point of sampling + title: surface material + examples: + - value: wood + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - material + - surface + slot_uri: MIXS:0000758 + multivalued: false + range: SURF_MATERIAL_ENUM + surf_moisture: + name: surf_moisture + annotations: + Preferred_unit: + tag: Preferred_unit + value: parts per million, gram per cubic meter, gram per square meter + description: Water held on a surface + title: surface moisture + examples: + - value: 0.01 gram per square meter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - moisture + - surface + slot_uri: MIXS:0000128 + multivalued: false + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + surf_moisture_ph: + name: surf_moisture_ph + description: ph measurement of surface + title: surface moisture pH + examples: + - value: '7' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - moisture + - ph + - surface + slot_uri: MIXS:0000760 + multivalued: false + range: float + recommended: true + surf_temp: + name: surf_temp + annotations: + Preferred_unit: + tag: Preferred_unit + value: degree Celsius + description: Temperature of the surface at the time of sampling + title: surface temperature + examples: + - value: 15 degree Celsius + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - surface + - temperature + slot_uri: MIXS:0000125 + multivalued: false + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + suspend_part_matter: + name: suspend_part_matter + annotations: + Preferred_unit: + tag: Preferred_unit + value: milligram per liter + description: Concentration of suspended particulate matter + title: suspended particulate matter + examples: + - value: 0.5 milligram per liter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - particle + - particulate + - suspended + slot_uri: MIXS:0000741 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + suspend_solids: + name: suspend_solids + annotations: + Expected_value: + tag: Expected_value + value: suspended solid name;measurement value + Preferred_unit: + tag: Preferred_unit + value: gram, microgram, milligram per liter, mole per liter, gram per liter, + part per million + description: Concentration of substances including a wide variety of material, + such as silt, decaying plant and animal matter; can include multiple substances + title: suspended solids + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - solids + - suspended + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000150 + multivalued: true + required: false + recommended: false + sym_life_cycle_type: + name: sym_life_cycle_type + annotations: + Expected_value: + tag: Expected_value + value: type of life cycle of the symbiotic organism (host of the samples) + description: Type of life cycle of the symbiotic host species (the thing being + sampled). Simple life cycles occur within a single host, complex ones within + multiple different hosts over the course of their normal life cycle + title: symbiotic host organism life cycle type + examples: + - value: complex life cycle + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - host + - host. + - life + - organism + - symbiosis + - type + slot_uri: MIXS:0001300 + multivalued: false + range: SYM_LIFE_CYCLE_TYPE_ENUM + required: true + symbiont_host_role: + name: symbiont_host_role + description: Role of the host in the life cycle of the symbiotic organism + title: host of the symbiont role + examples: + - value: intermediate + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - host + - host. + - symbiosis + slot_uri: MIXS:0001303 + multivalued: false + range: SYMBIONT_HOST_ROLE_ENUM + recommended: true + tan: + name: tan + annotations: + Preferred_unit: + tag: Preferred_unit + value: milligram per liter + description: 'Total Acid Number (TAN) is a measurement of acidity that is determined + by the amount of potassium hydroxide in milligrams that is needed to neutralize + the acids in one gram of oil. It is an important quality measurement of crude + oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)' + title: total acid number + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - number + - total + slot_uri: MIXS:0000120 + multivalued: false + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + target_gene: + name: target_gene + description: Targeted gene or locus name for marker gene studies + title: target gene + examples: + - value: 16S rRNA, 18S rRNA, nif, amoA, rpo + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - target + slot_uri: MIXS:0000044 + multivalued: false + range: string + target_subfragment: + name: target_subfragment + description: Name of subfragment of a gene or locus. Important to e.g. identify + special regions on marker genes like V6 on 16S rRNA + title: target subfragment + examples: + - value: V6, V9, ITS + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - target + slot_uri: MIXS:0000045 + multivalued: false + range: string + tax_class: + name: tax_class + description: Method used for taxonomic classification, along with reference database + used, classification rank, and thresholds used to classify new genomes + title: taxonomic classification + examples: + - value: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, + default parameters) + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - classification + - taxon + slot_uri: MIXS:0000064 + multivalued: false + range: string + tax_ident: + name: tax_ident + description: The phylogenetic marker(s) used to assign an organism name to the + SAG or MAG + title: taxonomic identity marker + examples: + - value: other + description: was other rpoB gene + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - identifier + - marker + - taxon + slot_uri: MIXS:0000053 + range: TAX_IDENT_ENUM + temp: + name: temp + annotations: + Preferred_unit: + tag: Preferred_unit + value: degree Celsius + description: Temperature of the sample at the time of sampling + title: temperature + examples: + - value: 25 degree Celsius + in_subset: + - environment + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - temperature + slot_uri: MIXS:0000113 + multivalued: false + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + temp_out: + name: temp_out + annotations: + Preferred_unit: + tag: Preferred_unit + value: degree Celsius + description: The recorded temperature value at sampling time outside + title: temperature outside house + examples: + - value: 5 degree Celsius + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - house + - temperature + slot_uri: MIXS:0000197 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tertiary_treatment: + name: tertiary_treatment + annotations: + Expected_value: + tag: Expected_value + value: tertiary treatment type + description: The process providing a final treatment stage to raise the effluent + quality before it is discharged to the receiving environment + title: tertiary treatment + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - treatment + string_serialization: '{text}' + slot_uri: MIXS:0000352 + multivalued: false + required: false + recommended: false + tidal_stage: + name: tidal_stage + description: Stage of tide + title: tidal stage + examples: + - value: high tide + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000750 + multivalued: false + range: TIDAL_STAGE_ENUM + required: false + recommended: false + tillage: + name: tillage + description: Note method(s) used for tilling + title: history/tillage + examples: + - value: chisel + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - history + slot_uri: MIXS:0001081 + multivalued: true + range: TILLAGE_ENUM + time_last_toothbrush: + name: time_last_toothbrush + description: Specification of the time since last toothbrushing + title: time since last toothbrushing + comments: + - P2H45M does not match ^P(?!$)(\\d+Y)?(\\d+M)?(\\d+W)?(\\d+D)?(T(?=\\d+[HMS])(\\d+H)?(\\d+M)?(\\d+S)?)?$ + - problematic ISO 8601 period validation + examples: + - value: PT2H45M + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - time + slot_uri: MIXS:0000924 + range: string + required: false + recommended: false + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true + time_since_last_wash: + name: time_since_last_wash + description: Specification of the time since last wash + title: time since last wash + examples: + - value: P1D + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - time + slot_uri: MIXS:0000943 + multivalued: false + range: string + required: false + recommended: false + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true + timepoint: + name: timepoint + annotations: + Preferred_unit: + tag: Preferred_unit + value: hours or days + description: Time point at which a sample or observation is made or taken from + a biomaterial as measured from some reference point. Indicate the timepoint + written in ISO 8601 format + title: timepoint + examples: + - value: PT24H + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - time + slot_uri: MIXS:0001173 + multivalued: false + range: string + required: false + recommended: false + pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$ + structured_pattern: + syntax: ^{duration}$ + interpolated: true + partial_match: true + tiss_cult_growth_med: + name: tiss_cult_growth_med + description: Description of plant tissue culture growth media used + title: tissue culture growth media + examples: + - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - culture + - growth + slot_uri: MIXS:0001070 + multivalued: false + range: string + required: false + recommended: false + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}|{text}$ + interpolated: true + partial_match: true + toluene: + name: toluene + annotations: + Preferred_unit: + tag: Preferred_unit + value: milligram per liter, parts per million + description: Concentration of toluene in the sample + title: toluene + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000154 + multivalued: false + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_carb: + name: tot_carb + description: Total carbon content + title: total carbon + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - carbon + - total + slot_uri: MIXS:0000525 + multivalued: false + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_depth_water_col: + name: tot_depth_water_col + annotations: + Preferred_unit: + tag: Preferred_unit + value: meter + description: Measurement of total depth of water column + title: total depth of water column + examples: + - value: 500 meter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - depth + - total + - water + slot_uri: MIXS:0000634 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_diss_nitro: + name: tot_diss_nitro + annotations: + Preferred_unit: + tag: Preferred_unit + value: microgram per liter + description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured + by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen' + title: total dissolved nitrogen + examples: + - value: 40 microgram per liter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - dissolved + - nitrogen + - total + slot_uri: MIXS:0000744 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_inorg_nitro: + name: tot_inorg_nitro + annotations: + Preferred_unit: + tag: Preferred_unit + value: microgram per liter + description: Total inorganic nitrogen content + title: total inorganic nitrogen + examples: + - value: 40 microgram per liter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - inorganic + - nitrogen + - total + slot_uri: MIXS:0000745 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_iron: + name: tot_iron + annotations: + Preferred_unit: + tag: Preferred_unit + value: milligram per liter, milligram per kilogram + description: Concentration of total iron in the sample + title: total iron + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - total + slot_uri: MIXS:0000105 + multivalued: false + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_nitro: + name: tot_nitro + annotations: + Preferred_unit: + tag: Preferred_unit + value: microgram per liter, micromole per liter, milligram per liter + description: 'Total nitrogen concentration of water samples, calculated by: total + nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured + without filtering, reported as nitrogen' + title: total nitrogen concentration + examples: + - value: 50 micromole per liter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - concentration + - nitrogen + - total + slot_uri: MIXS:0000102 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_nitro_cont_meth: + name: tot_nitro_cont_meth + description: Reference or method used in determining the total nitrogen + title: total nitrogen content method + examples: + - value: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - content + - method + - nitrogen + - total + slot_uri: MIXS:0000338 + multivalued: false + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + tot_nitro_content: + name: tot_nitro_content + description: Total nitrogen content of the sample + title: total nitrogen content + examples: + - value: 35 milligrams Nitrogen per kilogram of soil + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - content + - nitrogen + - total + slot_uri: MIXS:0000530 + multivalued: false + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_org_c_meth: + name: tot_org_c_meth + description: Reference or method used in determining total organic carbon + title: total organic carbon method + examples: + - value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - carbon + - method + - organic + - total + slot_uri: MIXS:0000337 + multivalued: false + range: string + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + tot_org_carb: + name: tot_org_carb + annotations: + Preferred_unit: + tag: Preferred_unit + value: gram Carbon per kilogram sample material + description: Total organic carbon content + title: total organic carbon + examples: + - value: '0.02' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - carbon + - organic + - total + slot_uri: MIXS:0000533 + multivalued: false + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_part_carb: + name: tot_part_carb + annotations: + Preferred_unit: + tag: Preferred_unit + value: microgram per liter, micromole per liter + description: Total particulate carbon content + title: total particulate carbon + examples: + - value: 35 micromole per liter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - carbon + - particle + - particulate + - total + slot_uri: MIXS:0000747 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_phosp: + name: tot_phosp + annotations: + Preferred_unit: + tag: Preferred_unit + value: micromole per liter, milligram per liter, parts per million + description: 'Total phosphorus concentration in the sample, calculated by: total + phosphorus = total dissolved phosphorus + particulate phosphorus' + title: total phosphorus + examples: + - value: 0.03 milligram per liter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - phosphorus + - total + slot_uri: MIXS:0000117 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_phosphate: + name: tot_phosphate + annotations: + Preferred_unit: + tag: Preferred_unit + value: microgram per liter, micromole per liter + description: Total amount or concentration of phosphate + title: total phosphate + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - phosphate + - total + slot_uri: MIXS:0000689 + multivalued: false + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tot_sulfur: + name: tot_sulfur + annotations: + Preferred_unit: + tag: Preferred_unit + value: milligram per liter, parts per million + description: Concentration of total sulfur in the sample + title: total sulfur + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - sulfur + - total + slot_uri: MIXS:0000419 + multivalued: false + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + train_line: + name: train_line + description: The subway line name + title: train line + examples: + - value: red + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - train + slot_uri: MIXS:0000837 + multivalued: false + range: TRAIN_LINE_ENUM + required: false + recommended: false + train_stat_loc: + name: train_stat_loc + description: The train station collection location + title: train station collection location + examples: + - value: forest hills + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - location + - train + slot_uri: MIXS:0000838 + multivalued: false + range: TRAIN_STAT_LOC_ENUM + required: false + recommended: false + train_stop_loc: + name: train_stop_loc + description: The train stop collection location + title: train stop collection location + examples: + - value: end + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - location + - stop + - train + slot_uri: MIXS:0000839 + multivalued: false + range: TRAIN_STOP_LOC_ENUM + required: false + recommended: false + travel_out_six_month: + name: travel_out_six_month + annotations: + Expected_value: + tag: Expected_value + value: country name + description: Specification of the countries travelled in the last six months; + can include multiple travels + title: travel outside the country in last six months + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - months + string_serialization: '{text}' + slot_uri: MIXS:0000268 + multivalued: true + required: false + recommended: false + trna_ext_software: + name: trna_ext_software + description: Tools used for tRNA identification + title: tRNA extraction software + examples: + - value: infernal;v2;default parameters + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - software + slot_uri: MIXS:0000068 + multivalued: false + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{software};{version};{parameters}$ + interpolated: true + partial_match: true + trnas: + name: trnas + annotations: + Expected_value: + tag: Expected_value + value: value from 0-21 + description: The total number of tRNAs identified from the SAG or MAG + title: number of standard tRNAs extracted + examples: + - value: '18' + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - number + string_serialization: '{integer}' + slot_uri: MIXS:0000067 + multivalued: false + trophic_level: + name: trophic_level + description: Trophic levels are the feeding position in a food chain. Microbes + can be a range of producers (e.g. chemolithotroph) + title: trophic level + examples: + - value: heterotroph + in_subset: + - nucleic acid sequence source + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - level + slot_uri: MIXS:0000032 + multivalued: false + range: TROPHIC_LEVEL_ENUM + turbidity: + name: turbidity + description: Measure of the amount of cloudiness or haziness in water caused by + individual particles + title: turbidity + examples: + - value: 0.3 nephelometric turbidity units + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000191 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tvdss_of_hcr_press: + name: tvdss_of_hcr_press + annotations: + Preferred_unit: + tag: Preferred_unit + value: meter + description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where + the original pressure was measured (e.g. 1578 m) + title: depth (TVDSS) of hydrocarbon resource pressure + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - depth + - hydrocarbon + - pressure + - resource + slot_uri: MIXS:0000397 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + tvdss_of_hcr_temp: + name: tvdss_of_hcr_temp + annotations: + Preferred_unit: + tag: Preferred_unit + value: meter + description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where + the original temperature was measured (e.g. 1345 m) + title: depth (TVDSS) of hydrocarbon resource temperature + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - depth + - hydrocarbon + - resource + - temperature + slot_uri: MIXS:0000394 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + twin_sibling: + name: twin_sibling + description: Specification of twin sibling presence + title: twin sibling presence + examples: + - value: 'yes' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - presence + slot_uri: MIXS:0000326 + multivalued: false + range: boolean + required: false + recommended: false + typ_occup_density: + name: typ_occup_density + description: Customary or normal density of occupants + title: typical occupant density + examples: + - value: '25' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - density + slot_uri: MIXS:0000771 + multivalued: false + range: float + required: true + type_of_symbiosis: + name: type_of_symbiosis + description: Type of biological interaction established between the symbiotic + host organism being sampled and its respective host + title: type of symbiosis + examples: + - value: parasitic + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - symbiosis + - type + slot_uri: MIXS:0001307 + multivalued: false + range: TYPE_OF_SYMBIOSIS_ENUM + recommended: true + urine_collect_meth: + name: urine_collect_meth + description: Specification of urine collection method + title: urine/collection method + examples: + - value: catheter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - method + slot_uri: MIXS:0000899 + multivalued: false + range: URINE_COLLECT_METH_ENUM + required: false + recommended: false + urobiom_sex: + name: urobiom_sex + annotations: + Expected_value: + tag: Expected_value + value: sex of the symbiotic organism (host of the samples); enumeration + description: Physical sex of the host + title: host sex + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - host + - host. + slot_uri: MIXS:0000862 + multivalued: false + range: UROBIOM_SEX_ENUM + required: false + recommended: false + urogenit_disord: + name: urogenit_disord + description: History of urogenital disorders, can include multiple disorders. + The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary + system disease (https://disease-ontology.org/?id=DOID:18) + title: urogenital disorder + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - disorder + slot_uri: MIXS:0000289 + multivalued: true + range: string + required: false + recommended: false + urogenit_tract_disor: + name: urogenit_tract_disor + description: History of urogenital tract disorders; can include multiple disorders. + The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, + urinary system disease (https://disease-ontology.org/?id=DOID:18) + title: urine/urogenital tract disorder + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - disorder + slot_uri: MIXS:0000278 + multivalued: true + range: string + required: false + recommended: false + ventilation_rate: + name: ventilation_rate + annotations: + Preferred_unit: + tag: Preferred_unit + value: cubic meter per minute, liters per second + description: Ventilation rate of the system in the sampled premises + title: ventilation rate + examples: + - value: 750 cubic meter per minute + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - rate + slot_uri: MIXS:0000114 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + ventilation_type: + name: ventilation_type + annotations: + Expected_value: + tag: Expected_value + value: ventilation type name + description: Ventilation system used in the sampled premises + title: ventilation type + examples: + - value: Operable windows + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - type + string_serialization: '{text}' + slot_uri: MIXS:0000756 + multivalued: true + vfa: + name: vfa + annotations: + Preferred_unit: + tag: Preferred_unit + value: milligram per liter, parts per million + description: Concentration of Volatile Fatty Acids in the sample + title: volatile fatty acids + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000152 + multivalued: false + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + vfa_fw: + name: vfa_fw + annotations: + Preferred_unit: + tag: Preferred_unit + value: milligram per liter + description: Original volatile fatty acid concentration in the hydrocarbon resource + title: vfa in formation water + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - water + slot_uri: MIXS:0000408 + multivalued: false + range: string + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + vir_ident_software: + name: vir_ident_software + annotations: + Expected_value: + tag: Expected_value + value: software name, version and relevant parameters + description: Tool(s) used for the identification of UViG as a viral genome, software + or protocol name including version number, parameters, and cutoffs used + title: viral identification software + examples: + - value: VirSorter; 1.0.4; Virome database, category 2 + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - identifier + - software + string_serialization: '{software};{version};{parameters}' + slot_uri: MIXS:0000081 + multivalued: false + virus_enrich_appr: + name: virus_enrich_appr + description: List of approaches used to enrich the sample for viruses, if any + title: virus enrichment approach + examples: + - value: filtration + description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse + - value: FeCl Precipitation + description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse + - value: ultracentrifugation + description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse + - value: DNAse + description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse + in_subset: + - nucleic acid sequence source + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - enrichment + slot_uri: MIXS:0000036 + range: VIRUS_ENRICH_APPR_ENUM + vis_media: + name: vis_media + annotations: + Expected_value: + tag: Expected_value + value: enumeration + description: The building visual media + title: visual media + examples: + - value: 3D scans + from_schema: https://w3id.org/mixs-6-2-rc + string_serialization: '[photos|videos|commonly of the building|site context (adjacent + buildings, vegetation, terrain, streets)|interiors|equipment|3D scans]' + slot_uri: MIXS:0000840 + multivalued: false + required: false + recommended: false + viscosity: + name: viscosity + annotations: + Expected_value: + tag: Expected_value + value: measurement value;measurement value + Preferred_unit: + tag: Preferred_unit + value: cP at degree Celsius + description: A measure of oil's resistance to gradual deformation by shear stress or tensile + stress (e.g. 3.5 cp; 100 C) + title: viscosity + from_schema: https://w3id.org/mixs-6-2-rc + string_serialization: '{float} {unit};{float} {unit}' + slot_uri: MIXS:0000126 + multivalued: false + required: false + recommended: false + volatile_org_comp: + name: volatile_org_comp + annotations: + Expected_value: + tag: Expected_value + value: volatile organic compound name;measurement value + Preferred_unit: + tag: Preferred_unit + value: microgram per cubic meter, parts per million, nanogram per liter + description: Concentration of carbon-based chemicals that easily evaporate at + room temperature; can report multiple volatile organic compounds by entering + numeric values preceded by name of compound + title: volatile organic compounds + examples: + - value: formaldehyde;500 nanogram per liter + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - organic + string_serialization: '{text};{float} {unit}' + slot_uri: MIXS:0000115 + multivalued: true + required: false + recommended: false + wall_area: + name: wall_area + annotations: + Preferred_unit: + tag: Preferred_unit + value: square meter + description: The total area of the sampled room's walls + title: wall area + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - area + - wall + slot_uri: MIXS:0000198 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + wall_const_type: + name: wall_const_type + description: The building class of the wall defined by the composition of the + building elements and fire-resistance rating + title: wall construction type + examples: + - value: fire resistive + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - type + - wall + slot_uri: MIXS:0000841 + multivalued: false + range: WALL_CONST_TYPE_ENUM + required: false + recommended: false + wall_finish_mat: + name: wall_finish_mat + description: The material utilized to finish the outer most layer of the wall + title: wall finish material + examples: + - value: wood + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - material + - wall + slot_uri: MIXS:0000842 + multivalued: false + range: WALL_FINISH_MAT_ENUM + required: false + recommended: false + wall_height: + name: wall_height + annotations: + Preferred_unit: + tag: Preferred_unit + value: centimeter + description: The average height of the walls in the sampled room + title: wall height + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - height + - wall + slot_uri: MIXS:0000221 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + wall_loc: + name: wall_loc + description: The relative location of the wall within the room + title: wall location + examples: + - value: north + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - location + - wall + slot_uri: MIXS:0000843 + multivalued: false + range: SHARED_ENUM_0 + required: false + recommended: false + wall_surf_treatment: + name: wall_surf_treatment + description: The surface treatment of interior wall + title: wall surface treatment + examples: + - value: paneling + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - surface + - treatment + - wall + slot_uri: MIXS:0000845 + multivalued: false + range: WALL_SURF_TREATMENT_ENUM + required: false + recommended: false + wall_texture: + name: wall_texture + description: The feel, appearance, or consistency of a wall surface + title: wall texture + examples: + - value: popcorn + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - texture + - wall + slot_uri: MIXS:0000846 + multivalued: false + range: SHARED_ENUM_4 + required: false + recommended: false + wall_thermal_mass: + name: wall_thermal_mass + annotations: + Preferred_unit: + tag: Preferred_unit + value: joule per degree Celsius + description: The ability of the wall to provide inertia against temperature fluctuations. + Generally this means concrete or concrete block that is either exposed or covered + only with paint + title: wall thermal mass + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - mass + - wall + slot_uri: MIXS:0000222 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + wall_water_mold: + name: wall_water_mold + description: Signs of the presence of mold or mildew on a wall + title: wall signs of water/mold + examples: + - value: no presence of mold visible + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - wall + slot_uri: MIXS:0000844 + multivalued: false + range: SHARED_ENUM_1 + required: false + recommended: false + wastewater_type: + name: wastewater_type + annotations: + Expected_value: + tag: Expected_value + value: wastewater type name + description: The origin of wastewater such as human waste, rainfall, storm drains, + etc + title: wastewater type + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - type + string_serialization: '{text}' + slot_uri: MIXS:0000353 + multivalued: false + required: false + recommended: false + water_cont_soil_meth: + name: water_cont_soil_meth + description: Reference or method used in determining the water content of soil + title: water content method + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - content + - method + - water + slot_uri: MIXS:0000323 + multivalued: false + range: string + required: false + recommended: false + pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$ + structured_pattern: + syntax: ^{PMID}|{DOI}|{URL}$ + interpolated: true + partial_match: true + water_content: + name: water_content + annotations: + Preferred_unit: + tag: Preferred_unit + value: gram per gram or cubic centimeter per cubic centimeter + description: Water content measurement + title: water content + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - content + - water + slot_uri: MIXS:0000185 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + water_current: + name: water_current + annotations: + Preferred_unit: + tag: Preferred_unit + value: cubic meter per second, knots + description: Measurement of magnitude and direction of flow within a fluid + title: water current + examples: + - value: 10 cubic meter per second + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - water + slot_uri: MIXS:0000203 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + water_cut: + name: water_cut + annotations: + Preferred_unit: + tag: Preferred_unit + value: percent + description: Current amount of water (%) in a produced fluid stream; or the average + of the combined streams + title: water cut + comments: + - percent or float? + examples: + - value: 45% + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - water + slot_uri: MIXS:0000454 + range: string + required: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + water_feat_size: + name: water_feat_size + annotations: + Preferred_unit: + tag: Preferred_unit + value: square meter + description: The size of the water feature + title: water feature size + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - feature + - size + - water + slot_uri: MIXS:0000223 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + water_feat_type: + name: water_feat_type + description: The type of water feature present within the building being sampled + title: water feature type + examples: + - value: stream + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - feature + - type + - water + slot_uri: MIXS:0000847 + multivalued: false + range: WATER_FEAT_TYPE_ENUM + required: false + recommended: false + water_frequency: + name: water_frequency + annotations: + Expected_value: + tag: Expected_value + value: rate + Preferred_unit: + tag: Preferred_unit + value: per day, per week, per month + description: Number of water delivery events within a given period of time + title: water delivery frequency + examples: + - value: 2 per day + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - delivery + - frequency + - water + string_serialization: '{float}{unit}' + slot_uri: MIXS:0001174 + multivalued: false + required: false + recommended: false + water_pH: + name: water_pH + title: water pH + examples: + - value: '7.2' + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - ph + - water + slot_uri: MIXS:0001175 + multivalued: false + range: float + required: false + recommended: false + water_prod_rate: + name: water_prod_rate + annotations: + Preferred_unit: + tag: Preferred_unit + value: cubic meter per day + description: Water production rates per well (e.g. 987 m3 / day) + title: water production rate + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - production + - rate + - water + slot_uri: MIXS:0000453 + multivalued: false + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + water_source_adjac: + name: water_source_adjac + annotations: + Expected_value: + tag: Expected_value + value: ENVO_01001110 or ENVO_00000070 + description: Description of the environmental features that are adjacent to the + farm water source. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) + and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple + terms can be separated by pipes + title: environmental feature adjacent water source + examples: + - value: feedlot [ENVO:01000627] + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - adjacent + - environmental + - feature + - source + - water + string_serialization: '{text}' + slot_uri: MIXS:0001122 + multivalued: true + required: false + recommended: false + water_source_shared: + name: water_source_shared + annotations: + Expected_value: + tag: Expected_value + value: enumeration + description: Other users sharing access to the same water source. Multiple terms + can be separated by one or more pipes + title: water source shared + examples: + - value: no sharing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - source + - water + string_serialization: '[multiple users, agricutural|multiple users, other|no sharing]' + slot_uri: MIXS:0001176 + multivalued: true + required: false + recommended: false + water_temp_regm: + name: water_temp_regm + annotations: + Preferred_unit: + tag: Preferred_unit + value: degree Celsius + description: Information about treatment involving an exposure to water with varying + degree of temperature, treatment regimen including how many times the treatment + was repeated, how long each treatment lasted, and the start and end time of + the entire treatment; can include multiple regimens + title: water temperature regimen + examples: + - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - regimen + - temperature + - water + slot_uri: MIXS:0000590 + multivalued: true + range: string + watering_regm: + name: watering_regm + annotations: + Preferred_unit: + tag: Preferred_unit + value: milliliter, liter + description: Information about treatment involving an exposure to watering frequencies, + treatment regimen including how many times the treatment was repeated, how long + each treatment lasted, and the start and end time of the entire treatment; can + include multiple regimens + title: watering regimen + examples: + - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - regimen + - water + slot_uri: MIXS:0000591 + multivalued: true + range: string + weekday: + name: weekday + description: The day of the week when sampling occurred + title: weekday + examples: + - value: Sunday + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000848 + multivalued: false + range: WEEKDAY_ENUM + required: false + recommended: false + weight_loss_3_month: + name: weight_loss_3_month + annotations: + Expected_value: + tag: Expected_value + value: weight loss specification;measurement value + Preferred_unit: + tag: Preferred_unit + value: kilogram, gram + description: Specification of weight loss in the last three months, if yes should + be further specified to include amount of weight loss + title: weight loss in last three months + examples: + - value: yes;5 kilogram + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - months + - weight + string_serialization: '{boolean};{float} {unit}' + slot_uri: MIXS:0000295 + multivalued: false + required: false + recommended: false + wga_amp_appr: + name: wga_amp_appr + description: Method used to amplify genomic DNA in preparation for sequencing + title: WGA amplification approach + examples: + - value: mda based + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000055 + multivalued: false + range: WGA_AMP_APPR_ENUM + wga_amp_kit: + name: wga_amp_kit + annotations: + Expected_value: + tag: Expected_value + value: kit name + description: Kit used to amplify genomic DNA in preparation for sequencing + title: WGA amplification kit + examples: + - value: qiagen repli-g + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - kit + string_serialization: '{text}' + slot_uri: MIXS:0000006 + multivalued: false + win: + name: win + description: 'A unique identifier of a well or wellbore. This is part of the Global + Framework for Well Identification initiative which is compiled by the Professional + Petroleum Data Management Association (PPDM) in an effort to improve well identification + systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)' + title: well identification number + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - identifier + - number + slot_uri: MIXS:0000297 + multivalued: false + range: string + recommended: true + wind_direction: + name: wind_direction + annotations: + Preferred_unit: + tag: Preferred_unit + value: degrees or cardinal direction + description: Wind direction is the direction from which a wind originates + title: wind direction + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - direction + - wind + slot_uri: MIXS:0000757 + multivalued: false + range: string + required: false + recommended: false + wind_speed: + name: wind_speed + description: speed of wind measured at the time of sampling + title: wind speed + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - speed + - wind + slot_uri: MIXS:0000118 + multivalued: false + range: string + required: false + recommended: false + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true + window_cond: + name: window_cond + description: The physical condition of the window at the time of sampling + title: window condition + examples: + - value: rupture + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - condition + - window + slot_uri: MIXS:0000849 + multivalued: false + range: SHARED_ENUM_2 + required: false + recommended: false + window_cover: + name: window_cover + description: The type of window covering + title: window covering + examples: + - value: curtains + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - window + slot_uri: MIXS:0000850 + multivalued: false + range: WINDOW_COVER_ENUM + required: false + recommended: false + window_horiz_pos: + name: window_horiz_pos + description: The horizontal position of the window on the wall + title: window horizontal position + examples: + - value: middle + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - window + slot_uri: MIXS:0000851 + multivalued: false + range: WINDOW_HORIZ_POS_ENUM + required: false + recommended: false + window_loc: + name: window_loc + description: The relative location of the window within the room + title: window location + examples: + - value: west + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - location + - window + slot_uri: MIXS:0000852 + multivalued: false + range: SHARED_ENUM_0 + required: false + recommended: false + window_mat: + name: window_mat + description: The type of material used to finish a window + title: window material + examples: + - value: wood + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - material + - window + slot_uri: MIXS:0000853 + multivalued: false + range: WINDOW_MAT_ENUM + required: false + recommended: false + window_open_freq: + name: window_open_freq + description: The number of times windows are opened per week + title: window open frequency + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - frequency + - window + slot_uri: MIXS:0000246 + multivalued: false + range: integer + required: false + recommended: false + window_size: + name: window_size + annotations: + Expected_value: + tag: Expected_value + value: measurement value + Preferred_unit: + tag: Preferred_unit + value: inch, meter + description: The window's length and width + title: window area/size + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - window + string_serialization: '{float} {unit} x {float} {unit}' + slot_uri: MIXS:0000224 + multivalued: false + required: false + recommended: false + window_status: + name: window_status + description: Defines whether the windows were open or closed during environmental + testing + title: window status + examples: + - value: open + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - status + - window + slot_uri: MIXS:0000855 + multivalued: false + range: WINDOW_STATUS_ENUM + required: false + recommended: false + window_type: + name: window_type + description: The type of windows + title: window type + examples: + - value: fixed window + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - type + - window + slot_uri: MIXS:0000856 + multivalued: false + range: WINDOW_TYPE_ENUM + required: false + recommended: false + window_vert_pos: + name: window_vert_pos + description: The vertical position of the window on the wall + title: window vertical position + examples: + - value: middle + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - window + slot_uri: MIXS:0000857 + multivalued: false + range: WINDOW_VERT_POS_ENUM + required: false + recommended: false + window_water_mold: + name: window_water_mold + description: Signs of the presence of mold or mildew on the window + title: window signs of water/mold + examples: + - value: no presence of mold visible + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - window + slot_uri: MIXS:0000854 + multivalued: false + range: SHARED_ENUM_1 + required: false + recommended: false + x16s_recover: + name: x16s_recover + description: Can a 16S gene be recovered from the submitted SAG or MAG? + title: 16S recovered + examples: + - value: 'yes' + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - recover + slot_uri: MIXS:0000065 + multivalued: false + range: boolean + x16s_recover_software: + name: x16s_recover_software + description: Tools used for 16S rRNA gene extraction + title: 16S recovery software + examples: + - value: rambl;v2;default parameters + in_subset: + - sequencing + from_schema: https://w3id.org/mixs-6-2-rc + keywords: + - recover + - software + slot_uri: MIXS:0000066 + multivalued: false + range: string + pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{software};{version};{parameters}$ + interpolated: true + partial_match: true + xylene: + name: xylene + annotations: + Preferred_unit: + tag: Preferred_unit + value: milligram per liter, parts per million + description: Concentration of xylene in the sample + title: xylene + from_schema: https://w3id.org/mixs-6-2-rc + slot_uri: MIXS:0000156 + multivalued: false + range: string + recommended: true + pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? + *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$ + structured_pattern: + syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$ + interpolated: true + partial_match: true +classes: + MigsBa: + name: MigsBa + description: 'Minimal Information about a Genome Sequence: cultured bacteria/archaea' + title: MIGS bacteria + from_schema: https://w3id.org/mixs-6-2-rc + aliases: + - migs_ba + is_a: Checklist + mixin: true + slots: + - samp_name + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - assembly_name + - temp + - compl_score + - nucl_acid_ext + - samp_size + - isol_growth_condt + - alt + - source_mat_id + - extrachrom_elements + - estimated_size + - samp_vol_we_dna_ext + - pathogenicity + - lib_reads_seqd + - rel_to_oxygen + - encoded_traits + - samp_collect_device + - number_contig + - biotic_relationship + - num_replicons + - lib_layout + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - host_spec_range + - neg_cont_type + - adapters + - assembly_software + - tax_ident + - annot + - trophic_level + - pos_cont_type + - subspecf_gen_lin + - feat_pred + - env_local_scale + - compl_software + - samp_mat_process + - sim_search_meth + - host_disease_stat + - depth + - samp_collect_method + - specific_host + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + name: adapters + recommended: true + alt: + name: alt + recommended: true + annot: + name: annot + recommended: true + assembly_name: + name: assembly_name + recommended: true + assembly_qual: + name: assembly_qual + required: true + assembly_software: + name: assembly_software + required: true + biotic_relationship: + name: biotic_relationship + recommended: true + compl_score: + name: compl_score + required: false + recommended: false + compl_software: + name: compl_software + required: false + recommended: false + depth: + name: depth + examples: + - value: 10 meter + recommended: true + elev: + name: elev + recommended: true + encoded_traits: + name: encoded_traits + required: false + recommended: false + estimated_size: + name: estimated_size + required: false + recommended: false + experimental_factor: + name: experimental_factor + required: false + recommended: false + extrachrom_elements: + name: extrachrom_elements + recommended: true + feat_pred: + name: feat_pred + required: false + recommended: false + host_disease_stat: + name: host_disease_stat + examples: + - value: rabies [DOID:11260] + recommended: true + host_spec_range: + name: host_spec_range + required: false + recommended: false + isol_growth_condt: + name: isol_growth_condt + required: true + lib_layout: + name: lib_layout + required: false + recommended: false + lib_reads_seqd: + name: lib_reads_seqd + required: false + recommended: false + lib_screen: + name: lib_screen + required: false + recommended: false + lib_size: + name: lib_size + required: false + recommended: false + lib_vector: + name: lib_vector + required: false + recommended: false + nucl_acid_amp: + name: nucl_acid_amp + recommended: true + nucl_acid_ext: + name: nucl_acid_ext + recommended: true + num_replicons: + name: num_replicons + required: true + number_contig: + name: number_contig + required: true + pathogenicity: + name: pathogenicity + recommended: true + ref_biomaterial: + name: ref_biomaterial + required: true + ref_db: + name: ref_db + required: false + recommended: false + rel_to_oxygen: + name: rel_to_oxygen + recommended: true + samp_collect_device: + name: samp_collect_device + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + required: false + recommended: false + samp_collect_method: + name: samp_collect_method + examples: + - value: swabbing + required: false + recommended: false + samp_mat_process: + name: samp_mat_process + required: false + recommended: false + samp_size: + name: samp_size + required: false + recommended: false + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: false + recommended: false + sim_search_meth: + name: sim_search_meth + required: false + recommended: false + sop: + name: sop + recommended: true + source_mat_id: + name: source_mat_id + recommended: true + specific_host: + name: specific_host + recommended: true + subspecf_gen_lin: + name: subspecf_gen_lin + recommended: true + tax_class: + name: tax_class + required: false + recommended: false + tax_ident: + name: tax_ident + recommended: true + temp: + name: temp + recommended: true + trophic_level: + name: trophic_level + recommended: true + class_uri: MIXS:0010003 + MigsEu: + name: MigsEu + description: 'Minimal Information about a Genome Sequence: eukaryote' + title: MIGS eukaryote + from_schema: https://w3id.org/mixs-6-2-rc + aliases: + - migs_eu + is_a: Checklist + mixin: true + slots: + - samp_name + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - assembly_name + - temp + - compl_score + - nucl_acid_ext + - samp_size + - isol_growth_condt + - alt + - estimated_size + - extrachrom_elements + - source_mat_id + - samp_vol_we_dna_ext + - ploidy + - pathogenicity + - lib_reads_seqd + - propagation + - samp_collect_device + - number_contig + - biotic_relationship + - num_replicons + - lib_layout + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - host_spec_range + - neg_cont_type + - adapters + - assembly_software + - tax_ident + - annot + - trophic_level + - pos_cont_type + - subspecf_gen_lin + - feat_pred + - env_local_scale + - compl_software + - samp_mat_process + - sim_search_meth + - host_disease_stat + - depth + - samp_collect_method + - specific_host + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + name: adapters + recommended: true + alt: + name: alt + recommended: true + annot: + name: annot + recommended: true + assembly_name: + name: assembly_name + recommended: true + assembly_qual: + name: assembly_qual + required: true + assembly_software: + name: assembly_software + required: true + biotic_relationship: + name: biotic_relationship + required: false + recommended: false + compl_score: + name: compl_score + required: false + recommended: false + compl_software: + name: compl_software + required: false + recommended: false + depth: + name: depth + examples: + - value: 10 meter + recommended: true + elev: + name: elev + recommended: true + estimated_size: + name: estimated_size + required: false + recommended: false + experimental_factor: + name: experimental_factor + required: false + recommended: false + extrachrom_elements: + name: extrachrom_elements + required: false + recommended: false + feat_pred: + name: feat_pred + required: false + recommended: false + host_disease_stat: + name: host_disease_stat + examples: + - value: rabies [DOID:11260] + required: false + recommended: false + host_spec_range: + name: host_spec_range + required: false + recommended: false + isol_growth_condt: + name: isol_growth_condt + required: true + lib_layout: + name: lib_layout + required: false + recommended: false + lib_reads_seqd: + name: lib_reads_seqd + required: false + recommended: false + lib_screen: + name: lib_screen + required: false + recommended: false + lib_size: + name: lib_size + required: false + recommended: false + lib_vector: + name: lib_vector + required: false + recommended: false + nucl_acid_amp: + name: nucl_acid_amp + recommended: true + nucl_acid_ext: + name: nucl_acid_ext + recommended: true + num_replicons: + name: num_replicons + required: false + recommended: false + number_contig: + name: number_contig + required: true + pathogenicity: + name: pathogenicity + recommended: true + ploidy: + name: ploidy + required: false + recommended: false + propagation: + name: propagation + recommended: true + ref_biomaterial: + name: ref_biomaterial + required: false + recommended: false + ref_db: + name: ref_db + required: false + recommended: false + samp_collect_device: + name: samp_collect_device + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + required: false + recommended: false + samp_collect_method: + name: samp_collect_method + examples: + - value: swabbing + required: false + recommended: false + samp_mat_process: + name: samp_mat_process + required: false + recommended: false + samp_size: + name: samp_size + required: false + recommended: false + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: false + recommended: false + sim_search_meth: + name: sim_search_meth + required: false + recommended: false + sop: + name: sop + recommended: true + source_mat_id: + name: source_mat_id + recommended: true + specific_host: + name: specific_host + required: false + recommended: false + subspecf_gen_lin: + name: subspecf_gen_lin + recommended: true + tax_class: + name: tax_class + required: false + recommended: false + tax_ident: + name: tax_ident + recommended: true + temp: + name: temp + recommended: true + trophic_level: + name: trophic_level + recommended: true + class_uri: MIXS:0010002 + MigsOrg: + name: MigsOrg + description: 'Minimal Information about a Genome Sequence: organelle' + title: MIGS org + from_schema: https://w3id.org/mixs-6-2-rc + aliases: + - migs_org + is_a: Checklist + mixin: true + slots: + - samp_name + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - assembly_name + - temp + - compl_score + - nucl_acid_ext + - samp_size + - isol_growth_condt + - alt + - source_mat_id + - extrachrom_elements + - estimated_size + - samp_vol_we_dna_ext + - lib_reads_seqd + - samp_collect_device + - number_contig + - lib_layout + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - adapters + - neg_cont_type + - assembly_software + - tax_ident + - annot + - pos_cont_type + - subspecf_gen_lin + - feat_pred + - env_local_scale + - compl_software + - samp_mat_process + - sim_search_meth + - depth + - samp_collect_method + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + name: adapters + recommended: true + alt: + name: alt + recommended: true + annot: + name: annot + recommended: true + assembly_name: + name: assembly_name + recommended: true + assembly_qual: + name: assembly_qual + required: false + recommended: false + assembly_software: + name: assembly_software + required: true + compl_score: + name: compl_score + required: false + recommended: false + compl_software: + name: compl_software + required: false + recommended: false + depth: + name: depth + examples: + - value: 10 meter + recommended: true + elev: + name: elev + recommended: true + estimated_size: + name: estimated_size + required: false + recommended: false + experimental_factor: + name: experimental_factor + required: false + recommended: false + extrachrom_elements: + name: extrachrom_elements + recommended: true + feat_pred: + name: feat_pred + required: false + recommended: false + isol_growth_condt: + name: isol_growth_condt + required: true + lib_layout: + name: lib_layout + required: false + recommended: false + lib_reads_seqd: + name: lib_reads_seqd + required: false + recommended: false + lib_screen: + name: lib_screen + required: false + recommended: false + lib_size: + name: lib_size + required: false + recommended: false + lib_vector: + name: lib_vector + required: false + recommended: false + nucl_acid_amp: + name: nucl_acid_amp + recommended: true + nucl_acid_ext: + name: nucl_acid_ext + recommended: true + number_contig: + name: number_contig + required: false + recommended: false + ref_biomaterial: + name: ref_biomaterial + required: false + recommended: false + ref_db: + name: ref_db + required: false + recommended: false + samp_collect_device: + name: samp_collect_device + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + required: false + recommended: false + samp_collect_method: + name: samp_collect_method + examples: + - value: swabbing + required: false + recommended: false + samp_mat_process: + name: samp_mat_process + required: false + recommended: false + samp_size: + name: samp_size + required: false + recommended: false + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: false + recommended: false + sim_search_meth: + name: sim_search_meth + required: false + recommended: false + sop: + name: sop + recommended: true + source_mat_id: + name: source_mat_id + recommended: true + subspecf_gen_lin: + name: subspecf_gen_lin + recommended: true + tax_class: + name: tax_class + required: false + recommended: false + tax_ident: + name: tax_ident + recommended: true + temp: + name: temp + recommended: true + class_uri: MIXS:0010006 + MigsPl: + name: MigsPl + description: 'Minimal Information about a Genome Sequence: plasmid' + title: MIGS pl + from_schema: https://w3id.org/mixs-6-2-rc + aliases: + - migs_pl + is_a: Checklist + mixin: true + slots: + - samp_name + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - assembly_name + - temp + - compl_score + - nucl_acid_ext + - samp_size + - isol_growth_condt + - alt + - source_mat_id + - estimated_size + - samp_vol_we_dna_ext + - lib_reads_seqd + - encoded_traits + - propagation + - samp_collect_device + - number_contig + - lib_layout + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - host_spec_range + - neg_cont_type + - adapters + - assembly_software + - tax_ident + - annot + - pos_cont_type + - subspecf_gen_lin + - feat_pred + - env_local_scale + - compl_software + - samp_mat_process + - sim_search_meth + - depth + - samp_collect_method + - specific_host + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + name: adapters + recommended: true + alt: + name: alt + recommended: true + annot: + name: annot + recommended: true + assembly_name: + name: assembly_name + recommended: true + assembly_qual: + name: assembly_qual + required: false + recommended: false + assembly_software: + name: assembly_software + required: true + compl_score: + name: compl_score + required: false + recommended: false + compl_software: + name: compl_software + required: false + recommended: false + depth: + name: depth + examples: + - value: 10 meter + recommended: true + elev: + name: elev + recommended: true + encoded_traits: + name: encoded_traits + recommended: true + estimated_size: + name: estimated_size + required: false + recommended: false + experimental_factor: + name: experimental_factor + required: false + recommended: false + feat_pred: + name: feat_pred + required: false + recommended: false + host_spec_range: + name: host_spec_range + required: false + recommended: false + isol_growth_condt: + name: isol_growth_condt + required: true + lib_layout: + name: lib_layout + required: false + recommended: false + lib_reads_seqd: + name: lib_reads_seqd + required: false + recommended: false + lib_screen: + name: lib_screen + required: false + recommended: false + lib_size: + name: lib_size + required: false + recommended: false + lib_vector: + name: lib_vector + required: false + recommended: false + nucl_acid_amp: + name: nucl_acid_amp + recommended: true + nucl_acid_ext: + name: nucl_acid_ext + recommended: true + number_contig: + name: number_contig + required: false + recommended: false + propagation: + name: propagation + required: true + ref_biomaterial: + name: ref_biomaterial + required: false + recommended: false + ref_db: + name: ref_db + required: false + recommended: false + samp_collect_device: + name: samp_collect_device + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + required: false + recommended: false + samp_collect_method: + name: samp_collect_method + examples: + - value: swabbing + required: false + recommended: false + samp_mat_process: + name: samp_mat_process + required: false + recommended: false + samp_size: + name: samp_size + required: false + recommended: false + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: false + recommended: false + sim_search_meth: + name: sim_search_meth + required: false + recommended: false + sop: + name: sop + recommended: true + source_mat_id: + name: source_mat_id + recommended: true + specific_host: + name: specific_host + recommended: true + subspecf_gen_lin: + name: subspecf_gen_lin + recommended: true + tax_class: + name: tax_class + required: false + recommended: false + tax_ident: + name: tax_ident + recommended: true + temp: + name: temp + recommended: true + class_uri: MIXS:0010004 + MigsVi: + name: MigsVi + description: 'Minimal Information about a Genome Sequence: virus' + title: MIGS virus + from_schema: https://w3id.org/mixs-6-2-rc + aliases: + - migs_vi + is_a: Checklist + mixin: true + slots: + - samp_name + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - assembly_name + - temp + - compl_score + - nucl_acid_ext + - samp_size + - isol_growth_condt + - alt + - source_mat_id + - estimated_size + - samp_vol_we_dna_ext + - pathogenicity + - lib_reads_seqd + - encoded_traits + - propagation + - samp_collect_device + - number_contig + - biotic_relationship + - num_replicons + - lib_layout + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - host_spec_range + - neg_cont_type + - virus_enrich_appr + - adapters + - assembly_software + - tax_ident + - annot + - pos_cont_type + - subspecf_gen_lin + - feat_pred + - env_local_scale + - compl_software + - samp_mat_process + - sim_search_meth + - host_disease_stat + - depth + - samp_collect_method + - specific_host + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + name: adapters + recommended: true + alt: + name: alt + recommended: true + annot: + name: annot + recommended: true + assembly_name: + name: assembly_name + recommended: true + assembly_qual: + name: assembly_qual + required: false + recommended: false + assembly_software: + name: assembly_software + required: true + biotic_relationship: + name: biotic_relationship + required: false + recommended: false + compl_score: + name: compl_score + required: false + recommended: false + compl_software: + name: compl_software + required: false + recommended: false + depth: + name: depth + examples: + - value: 10 meter + recommended: true + elev: + name: elev + recommended: true + encoded_traits: + name: encoded_traits + recommended: true + estimated_size: + name: estimated_size + required: false + recommended: false + experimental_factor: + name: experimental_factor + required: false + recommended: false + feat_pred: + name: feat_pred + required: false + recommended: false + host_disease_stat: + name: host_disease_stat + examples: + - value: rabies [DOID:11260] + recommended: true + host_spec_range: + name: host_spec_range + recommended: true + isol_growth_condt: + name: isol_growth_condt + required: true + lib_layout: + name: lib_layout + required: false + recommended: false + lib_reads_seqd: + name: lib_reads_seqd + required: false + recommended: false + lib_screen: + name: lib_screen + required: false + recommended: false + lib_size: + name: lib_size + required: false + recommended: false + lib_vector: + name: lib_vector + required: false + recommended: false + nucl_acid_amp: + name: nucl_acid_amp + recommended: true + nucl_acid_ext: + name: nucl_acid_ext + recommended: true + num_replicons: + name: num_replicons + recommended: true + number_contig: + name: number_contig + required: false + recommended: false + pathogenicity: + name: pathogenicity + recommended: true + propagation: + name: propagation + required: true + ref_biomaterial: + name: ref_biomaterial + required: false + recommended: false + ref_db: + name: ref_db + required: false + recommended: false + samp_collect_device: + name: samp_collect_device + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + required: false + recommended: false + samp_collect_method: + name: samp_collect_method + examples: + - value: swabbing + required: false + recommended: false + samp_mat_process: + name: samp_mat_process + required: false + recommended: false + samp_size: + name: samp_size + required: false + recommended: false + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: false + recommended: false + sim_search_meth: + name: sim_search_meth + required: false + recommended: false + sop: + name: sop + recommended: true + source_mat_id: + name: source_mat_id + recommended: true + specific_host: + name: specific_host + recommended: true + subspecf_gen_lin: + name: subspecf_gen_lin + recommended: true + tax_class: + name: tax_class + required: false + recommended: false + tax_ident: + name: tax_ident + recommended: true + temp: + name: temp + recommended: true + virus_enrich_appr: + name: virus_enrich_appr + recommended: true + class_uri: MIXS:0010005 + Mimag: + name: Mimag + description: Minimum Information About a Metagenome-Assembled Genome + title: MIMAG + from_schema: https://w3id.org/mixs-6-2-rc + aliases: + - mimag + is_a: Checklist + mixin: true + slots: + - samp_name + - size_frac + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - contam_screen_input + - mid + - assembly_name + - temp + - compl_score + - trnas + - mag_cov_software + - nucl_acid_ext + - samp_size + - alt + - bin_param + - bin_software + - source_mat_id + - samp_vol_we_dna_ext + - lib_reads_seqd + - rel_to_oxygen + - reassembly_bin + - decontam_software + - samp_collect_device + - number_contig + - trna_ext_software + - lib_layout + - contam_screen_param + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - adapters + - neg_cont_type + - assembly_software + - tax_ident + - contam_score + - annot + - x16s_recover_software + - x16s_recover + - pos_cont_type + - feat_pred + - compl_software + - env_local_scale + - samp_mat_process + - sim_search_meth + - depth + - samp_collect_method + - compl_appr + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + name: adapters + recommended: true + alt: + name: alt + recommended: true + annot: + name: annot + required: false + recommended: false + assembly_name: + name: assembly_name + recommended: true + assembly_qual: + name: assembly_qual + required: true + assembly_software: + name: assembly_software + required: true + bin_param: + name: bin_param + required: true + bin_software: + name: bin_software + required: true + compl_appr: + name: compl_appr + required: false + recommended: false + compl_score: + name: compl_score + required: true + compl_software: + name: compl_software + required: true + contam_score: + name: contam_score + required: true + contam_screen_input: + name: contam_screen_input + required: false + recommended: false + contam_screen_param: + name: contam_screen_param + required: false + recommended: false + decontam_software: + name: decontam_software + required: false + recommended: false + depth: + name: depth + examples: + - value: 10 meter + recommended: true + elev: + name: elev + recommended: true + experimental_factor: + name: experimental_factor + recommended: true + feat_pred: + name: feat_pred + required: false + recommended: false + lib_layout: + name: lib_layout + recommended: true + lib_reads_seqd: + name: lib_reads_seqd + recommended: true + lib_screen: + name: lib_screen + recommended: true + lib_size: + name: lib_size + recommended: true + lib_vector: + name: lib_vector + recommended: true + mag_cov_software: + name: mag_cov_software + required: false + recommended: false + mid: + name: mid + recommended: true + nucl_acid_amp: + name: nucl_acid_amp + recommended: true + nucl_acid_ext: + name: nucl_acid_ext + recommended: true + number_contig: + name: number_contig + required: false + recommended: false + reassembly_bin: + name: reassembly_bin + required: false + recommended: false + ref_biomaterial: + name: ref_biomaterial + required: false + recommended: false + ref_db: + name: ref_db + required: false + recommended: false + rel_to_oxygen: + name: rel_to_oxygen + required: false + recommended: false + samp_collect_device: + name: samp_collect_device + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + recommended: true + samp_collect_method: + name: samp_collect_method + examples: + - value: swabbing + recommended: true + samp_mat_process: + name: samp_mat_process + recommended: true + samp_size: + name: samp_size + recommended: true + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: false + recommended: false + sim_search_meth: + name: sim_search_meth + required: false + recommended: false + size_frac: + name: size_frac + required: false + recommended: false + sop: + name: sop + recommended: true + source_mat_id: + name: source_mat_id + recommended: true + tax_class: + name: tax_class + required: false + recommended: false + tax_ident: + name: tax_ident + required: true + temp: + name: temp + recommended: true + trna_ext_software: + name: trna_ext_software + required: false + recommended: false + trnas: + name: trnas + required: false + recommended: false + x16s_recover: + name: x16s_recover + required: false + recommended: false + x16s_recover_software: + name: x16s_recover_software + required: false + recommended: false + class_uri: MIXS:0010011 + MimarksC: + name: MimarksC + description: 'Minimal Information about a Marker Specimen: specimen' + title: MIMARKS specimen + comments: + - for marker gene sequences from cultured or voucher-identifiable specimens + from_schema: https://w3id.org/mixs-6-2-rc + aliases: + - mimarks_c + - MIMARKS-SU + - MIMARKS-specimen + is_a: Checklist + mixin: true + slots: + - samp_name + - pcr_primers + - nucl_acid_amp + - target_subfragment + - temp + - pcr_cond + - nucl_acid_ext + - samp_size + - isol_growth_condt + - alt + - source_mat_id + - extrachrom_elements + - samp_vol_we_dna_ext + - rel_to_oxygen + - samp_collect_device + - biotic_relationship + - seq_quality_check + - project_name + - neg_cont_type + - chimera_check + - trophic_level + - pos_cont_type + - subspecf_gen_lin + - env_local_scale + - samp_mat_process + - depth + - samp_collect_method + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - experimental_factor + - target_gene + - associated_resource + - sop + slot_usage: + alt: + name: alt + recommended: true + biotic_relationship: + name: biotic_relationship + recommended: true + chimera_check: + name: chimera_check + recommended: true + depth: + name: depth + examples: + - value: 10 meter + recommended: true + elev: + name: elev + recommended: true + experimental_factor: + name: experimental_factor + required: false + recommended: false + extrachrom_elements: + name: extrachrom_elements + required: false + recommended: false + isol_growth_condt: + name: isol_growth_condt + required: true + nucl_acid_amp: + name: nucl_acid_amp + recommended: true + nucl_acid_ext: + name: nucl_acid_ext + recommended: true + pcr_cond: + name: pcr_cond + recommended: true + pcr_primers: + name: pcr_primers + recommended: true + rel_to_oxygen: + name: rel_to_oxygen + recommended: true + samp_collect_device: + name: samp_collect_device + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + required: false + recommended: false + samp_collect_method: + name: samp_collect_method + examples: + - value: swabbing + required: false + recommended: false + samp_mat_process: + name: samp_mat_process + recommended: true + samp_size: + name: samp_size + required: false + recommended: false + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: false + recommended: false + seq_quality_check: + name: seq_quality_check + recommended: true + sop: + name: sop + recommended: true + source_mat_id: + name: source_mat_id + recommended: true + subspecf_gen_lin: + name: subspecf_gen_lin + recommended: true + target_gene: + name: target_gene + required: true + target_subfragment: + name: target_subfragment + recommended: true + temp: + name: temp + recommended: true + trophic_level: + name: trophic_level + recommended: true + class_uri: MIXS:0010009 + MimarksS: + name: MimarksS + description: 'Minimal Information about a Marker Specimen: survey' + title: MIMARKS survey + comments: + - for marker gene sequences obtained directly from the environment + from_schema: https://w3id.org/mixs-6-2-rc + aliases: + - mimarks_s + - MIMARKS-SP + - MIMARKS-survey + is_a: Checklist + mixin: true + slots: + - samp_name + - pcr_primers + - size_frac + - lib_screen + - nucl_acid_amp + - lib_size + - target_subfragment + - mid + - temp + - nucl_acid_ext + - samp_size + - alt + - source_mat_id + - samp_vol_we_dna_ext + - lib_reads_seqd + - rel_to_oxygen + - samp_collect_device + - seq_quality_check + - lib_layout + - env_broad_scale + - project_name + - lib_vector + - adapters + - neg_cont_type + - assembly_software + - chimera_check + - pos_cont_type + - env_local_scale + - samp_mat_process + - depth + - samp_collect_method + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - pcr_cond + - experimental_factor + - target_gene + - associated_resource + - sop + slot_usage: + adapters: + name: adapters + recommended: true + alt: + name: alt + recommended: true + assembly_software: + name: assembly_software + recommended: true + chimera_check: + name: chimera_check + recommended: true + depth: + name: depth + examples: + - value: 10 meter + recommended: true + elev: + name: elev + recommended: true + experimental_factor: + name: experimental_factor + recommended: true + lib_layout: + name: lib_layout + recommended: true + lib_reads_seqd: + name: lib_reads_seqd + recommended: true + lib_screen: + name: lib_screen + recommended: true + lib_size: + name: lib_size + recommended: true + lib_vector: + name: lib_vector + recommended: true + mid: + name: mid + recommended: true + nucl_acid_amp: + name: nucl_acid_amp + recommended: true + nucl_acid_ext: + name: nucl_acid_ext + recommended: true + pcr_cond: + name: pcr_cond + recommended: true + pcr_primers: + name: pcr_primers + recommended: true + rel_to_oxygen: + name: rel_to_oxygen + required: false + recommended: false + samp_collect_device: + name: samp_collect_device + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + recommended: true + samp_collect_method: + name: samp_collect_method + examples: + - value: swabbing + recommended: true + samp_mat_process: + name: samp_mat_process + recommended: true + samp_size: + name: samp_size + recommended: true + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: false + recommended: false + seq_quality_check: + name: seq_quality_check + recommended: true + size_frac: + name: size_frac + required: false + recommended: false + sop: + name: sop + recommended: true + source_mat_id: + name: source_mat_id + recommended: true + target_gene: + name: target_gene + required: true + target_subfragment: + name: target_subfragment + recommended: true + temp: + name: temp + recommended: true + class_uri: MIXS:0010008 + Mims: + name: Mims + description: Metagenome or Environmental + title: MIMS + from_schema: https://w3id.org/mixs-6-2-rc + aliases: + - mims + is_a: Checklist + mixin: true + slots: + - samp_name + - size_frac + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - mid + - assembly_name + - temp + - nucl_acid_ext + - samp_size + - alt + - source_mat_id + - samp_vol_we_dna_ext + - lib_reads_seqd + - rel_to_oxygen + - samp_collect_device + - number_contig + - lib_layout + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - adapters + - neg_cont_type + - assembly_software + - annot + - pos_cont_type + - feat_pred + - env_local_scale + - samp_mat_process + - sim_search_meth + - depth + - samp_collect_method + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + name: adapters + recommended: true + alt: + name: alt + recommended: true + annot: + name: annot + recommended: true + assembly_name: + name: assembly_name + recommended: true + assembly_qual: + name: assembly_qual + recommended: true + assembly_software: + name: assembly_software + recommended: true + depth: + name: depth + examples: + - value: 10 meter + recommended: true + elev: + name: elev + recommended: true + experimental_factor: + name: experimental_factor + recommended: true + feat_pred: + name: feat_pred + required: false + recommended: false + lib_layout: + name: lib_layout + recommended: true + lib_reads_seqd: + name: lib_reads_seqd + recommended: true + lib_screen: + name: lib_screen + recommended: true + lib_size: + name: lib_size + recommended: true + lib_vector: + name: lib_vector + recommended: true + mid: + name: mid + recommended: true + nucl_acid_amp: + name: nucl_acid_amp + recommended: true + nucl_acid_ext: + name: nucl_acid_ext + recommended: true + number_contig: + name: number_contig + recommended: true + ref_biomaterial: + name: ref_biomaterial + required: false + recommended: false + ref_db: + name: ref_db + required: false + recommended: false + rel_to_oxygen: + name: rel_to_oxygen + required: false + recommended: false + samp_collect_device: + name: samp_collect_device + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + recommended: true + samp_collect_method: + name: samp_collect_method + examples: + - value: swabbing + recommended: true + samp_mat_process: + name: samp_mat_process + recommended: true + samp_size: + name: samp_size + recommended: true + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: false + recommended: false + sim_search_meth: + name: sim_search_meth + required: false + recommended: false + size_frac: + name: size_frac + required: false + recommended: false + sop: + name: sop + recommended: true + source_mat_id: + name: source_mat_id + recommended: true + tax_class: + name: tax_class + required: false + recommended: false + temp: + name: temp + recommended: true + class_uri: MIXS:0010007 + Misag: + name: Misag + description: Minimum Information About a Single Amplified Genome + title: Minimum Information About a Single Amplified Genome + from_schema: https://w3id.org/mixs-6-2-rc + aliases: + - misag + is_a: Checklist + mixin: true + slots: + - samp_name + - size_frac + - lib_screen + - ref_db + - nucl_acid_amp + - lib_size + - contam_screen_input + - mid + - assembly_name + - temp + - compl_score + - trnas + - nucl_acid_ext + - samp_size + - alt + - source_mat_id + - samp_vol_we_dna_ext + - lib_reads_seqd + - rel_to_oxygen + - wga_amp_kit + - decontam_software + - samp_collect_device + - number_contig + - trna_ext_software + - sc_lysis_method + - lib_layout + - contam_screen_param + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - adapters + - neg_cont_type + - assembly_software + - tax_ident + - contam_score + - annot + - x16s_recover_software + - x16s_recover + - pos_cont_type + - feat_pred + - compl_software + - env_local_scale + - sort_tech + - samp_mat_process + - sim_search_meth + - depth + - samp_collect_method + - wga_amp_appr + - compl_appr + - env_medium + - samp_taxon_id + - geo_loc_name + - sc_lysis_approach + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - associated_resource + - sop + slot_usage: + adapters: + name: adapters + recommended: true + alt: + name: alt + recommended: true + annot: + name: annot + required: false + recommended: false + assembly_name: + name: assembly_name + recommended: true + assembly_qual: + name: assembly_qual + required: true + assembly_software: + name: assembly_software + required: true + compl_appr: + name: compl_appr + required: false + recommended: false + compl_score: + name: compl_score + required: true + compl_software: + name: compl_software + required: true + contam_score: + name: contam_score + required: true + contam_screen_input: + name: contam_screen_input + required: false + recommended: false + contam_screen_param: + name: contam_screen_param + required: false + recommended: false + decontam_software: + name: decontam_software + required: false + recommended: false + depth: + name: depth + examples: + - value: 10 meter + recommended: true + elev: + name: elev + recommended: true + experimental_factor: + name: experimental_factor + recommended: true + feat_pred: + name: feat_pred + required: false + recommended: false + lib_layout: + name: lib_layout + recommended: true + lib_reads_seqd: + name: lib_reads_seqd + recommended: true + lib_screen: + name: lib_screen + recommended: true + lib_size: + name: lib_size + recommended: true + lib_vector: + name: lib_vector + recommended: true + mid: + name: mid + recommended: true + nucl_acid_amp: + name: nucl_acid_amp + recommended: true + nucl_acid_ext: + name: nucl_acid_ext + recommended: true + number_contig: + name: number_contig + required: false + recommended: false + ref_biomaterial: + name: ref_biomaterial + required: false + recommended: false + ref_db: + name: ref_db + required: false + recommended: false + rel_to_oxygen: + name: rel_to_oxygen + required: false + recommended: false + samp_collect_device: + name: samp_collect_device + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + recommended: true + samp_collect_method: + name: samp_collect_method + examples: + - value: swabbing + recommended: true + samp_mat_process: + name: samp_mat_process + recommended: true + samp_size: + name: samp_size + recommended: true + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: false + recommended: false + sc_lysis_approach: + name: sc_lysis_approach + required: true + sc_lysis_method: + name: sc_lysis_method + required: false + recommended: false + sim_search_meth: + name: sim_search_meth + required: false + recommended: false + size_frac: + name: size_frac + required: false + recommended: false + sop: + name: sop + recommended: true + sort_tech: + name: sort_tech + required: true + source_mat_id: + name: source_mat_id + recommended: true + tax_class: + name: tax_class + required: false + recommended: false + tax_ident: + name: tax_ident + required: true + temp: + name: temp + recommended: true + trna_ext_software: + name: trna_ext_software + required: false + recommended: false + trnas: + name: trnas + required: false + recommended: false + wga_amp_appr: + name: wga_amp_appr + required: true + wga_amp_kit: + name: wga_amp_kit + required: false + recommended: false + x16s_recover: + name: x16s_recover + required: false + recommended: false + x16s_recover_software: + name: x16s_recover_software + required: false + recommended: false + class_uri: MIXS:0010010 + Miuvig: + name: Miuvig + description: Minimum Information About an Uncultivated Virus Genome + title: Minimum Information About an Uncultivated Virus Genome + from_schema: https://w3id.org/mixs-6-2-rc + aliases: + - miuvig + is_a: Checklist + mixin: true + slots: + - samp_name + - size_frac + - lib_screen + - source_uvig + - ref_db + - nucl_acid_amp + - lib_size + - mid + - assembly_name + - temp + - compl_score + - trnas + - nucl_acid_ext + - samp_size + - alt + - estimated_size + - source_mat_id + - samp_vol_we_dna_ext + - pathogenicity + - lib_reads_seqd + - samp_collect_device + - number_contig + - biotic_relationship + - trna_ext_software + - lib_layout + - assembly_qual + - ref_biomaterial + - project_name + - lib_vector + - host_spec_range + - neg_cont_type + - virus_enrich_appr + - adapters + - assembly_software + - tax_ident + - annot + - pos_cont_type + - feat_pred + - compl_software + - env_local_scale + - samp_mat_process + - sim_search_meth + - host_disease_stat + - depth + - samp_collect_method + - compl_appr + - specific_host + - env_medium + - samp_taxon_id + - geo_loc_name + - collection_date + - seq_meth + - lat_lon + - elev + - env_broad_scale + - tax_class + - experimental_factor + - sort_tech + - sc_lysis_approach + - sc_lysis_method + - wga_amp_appr + - wga_amp_kit + - bin_param + - bin_software + - reassembly_bin + - mag_cov_software + - vir_ident_software + - pred_genome_type + - pred_genome_struc + - detec_type + - otu_class_appr + - otu_seq_comp_appr + - otu_db + - host_pred_appr + - host_pred_est_acc + - associated_resource + - sop + slot_usage: + adapters: + name: adapters + recommended: true + alt: + name: alt + recommended: true + annot: + name: annot + required: false + recommended: false + assembly_name: + name: assembly_name + recommended: true + assembly_qual: + name: assembly_qual + required: true + assembly_software: + name: assembly_software + required: true + bin_param: + name: bin_param + recommended: true + bin_software: + name: bin_software + recommended: true + biotic_relationship: + name: biotic_relationship + required: false + recommended: false + compl_appr: + name: compl_appr + recommended: true + compl_score: + name: compl_score + recommended: true + compl_software: + name: compl_software + required: false + recommended: false + depth: + name: depth + examples: + - value: 10 meter + recommended: true + detec_type: + name: detec_type + required: true + elev: + name: elev + recommended: true + estimated_size: + name: estimated_size + required: false + recommended: false + experimental_factor: + name: experimental_factor + recommended: true + feat_pred: + name: feat_pred + recommended: true + host_disease_stat: + name: host_disease_stat + examples: + - value: rabies [DOID:11260] + recommended: true + host_pred_appr: + name: host_pred_appr + recommended: true + host_pred_est_acc: + name: host_pred_est_acc + recommended: true + host_spec_range: + name: host_spec_range + required: false + recommended: false + lib_layout: + name: lib_layout + recommended: true + lib_reads_seqd: + name: lib_reads_seqd + recommended: true + lib_screen: + name: lib_screen + recommended: true + lib_size: + name: lib_size + recommended: true + lib_vector: + name: lib_vector + recommended: true + mag_cov_software: + name: mag_cov_software + required: false + recommended: false + mid: + name: mid + recommended: true + nucl_acid_amp: + name: nucl_acid_amp + recommended: true + nucl_acid_ext: + name: nucl_acid_ext + recommended: true + number_contig: + name: number_contig + required: true + otu_class_appr: + name: otu_class_appr + recommended: true + otu_db: + name: otu_db + recommended: true + otu_seq_comp_appr: + name: otu_seq_comp_appr + recommended: true + pathogenicity: + name: pathogenicity + required: false + recommended: false + pred_genome_struc: + name: pred_genome_struc + required: true + pred_genome_type: + name: pred_genome_type + required: true + reassembly_bin: + name: reassembly_bin + recommended: true + ref_biomaterial: + name: ref_biomaterial + required: false + recommended: false + ref_db: + name: ref_db + recommended: true + samp_collect_device: + name: samp_collect_device + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + recommended: true + samp_collect_method: + name: samp_collect_method + examples: + - value: swabbing + recommended: true + samp_mat_process: + name: samp_mat_process + recommended: true + samp_size: + name: samp_size + recommended: true + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: false + recommended: false + sc_lysis_approach: + name: sc_lysis_approach + recommended: true + sc_lysis_method: + name: sc_lysis_method + recommended: true + sim_search_meth: + name: sim_search_meth + recommended: true + size_frac: + name: size_frac + recommended: true + sop: + name: sop + recommended: true + sort_tech: + name: sort_tech + recommended: true + source_mat_id: + name: source_mat_id + recommended: true + source_uvig: + name: source_uvig + required: true + specific_host: + name: specific_host + required: false + recommended: false + tax_class: + name: tax_class + recommended: true + tax_ident: + name: tax_ident + required: false + recommended: false + temp: + name: temp + recommended: true + trna_ext_software: + name: trna_ext_software + required: false + recommended: false + trnas: + name: trnas + required: false + recommended: false + vir_ident_software: + name: vir_ident_software + required: true + virus_enrich_appr: + name: virus_enrich_appr + required: true + wga_amp_appr: + name: wga_amp_appr + recommended: true + wga_amp_kit: + name: wga_amp_kit + recommended: true + class_uri: MIXS:0010012 + Agriculture: + name: Agriculture + description: agriculture extension + title: agriculture + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Extension + slots: + - plant_growth_med + - photosynt_activ + - photosynt_activ_meth + - samp_collect_method - enrichment_protocol - library_prep_kit - sequencing_location @@ -20154,848 +22974,1451 @@ classes: - host_symbiont - host_disease_stat - pres_animal_insect - - plant_water_method - - anim_water_method - - farm_water_source - - water_source_shared - - water_pH - - elev + - plant_water_method + - anim_water_method + - farm_water_source + - water_source_shared + - water_pH + - elev + - season + - solar_irradiance + - crop_yield + - season_humidity + - humidity + - adjacent_environment + - chem_administration + - food_prod + - lot_number + - fertilizer_admin + - samp_store_temp + - food_trav_mode + - food_trav_vehic + - farm_equip_san + - farm_equip + - farm_equip_shared + - food_harvest_proc + - plant_struc + - host_dry_mass + - ances_data + - genetic_mod + - food_product_type + - food_source + - spikein_strain + - organism_count + - size_frac_low + - size_frac_up + - cult_isol_date + - samp_pooling + - root_med_macronutr + - root_med_carbon + - root_med_ph + - depth + - specific_host + - pathogenicity + - biotic_relationship + - water_temp_regm + - watering_regm + - standing_water_regm + - gaseous_environment + - fungicide_regm + - climate_environment + - herbicide_regm + - non_min_nutr_regm + - pesticide_regm + - ph_regm + - salt_regm + - season_environment + - temp + - perturbation + - isol_growth_condt + - samp_store_dur + - samp_store_loc + - samp_collect_device + - samp_mat_process + - host_age + - host_common_name + - host_genotype + - host_height + - host_subspecf_genlin + - host_length + - host_life_stage + - host_phenotype + - host_taxid + - host_tot_mass + - host_spec_range + - trophic_level + - plant_product + - samp_size + - oxy_stat_samp + - seq_meth + - samp_vol_we_dna_ext + - pcr_primers + - nucl_acid_ext + - nucl_acid_amp + - lib_size + - lib_reads_seqd + - lib_layout + - lib_vector + - lib_screen + - target_gene + - target_subfragment + - mid + - adapters + - pcr_cond + - seq_quality_check + - chimera_check + - assembly_name + - assembly_qual + - assembly_software + - annot + - associated_resource + - sop + - source_mat_id + - fao_class + - local_class + - local_class_meth + - soil_type + - soil_type_meth + - soil_horizon + - horizon_meth + - link_class_info + - previous_land_use + - prev_land_use_meth + - crop_rotation + - agrochem_addition + - tillage + - fire + - flooding + - extreme_event + - link_climate_info + - annual_temp + - season_temp + - annual_precpt + - season_precpt + - cur_land_use + - slope_gradient + - slope_aspect + - profile_position + - drainage_class + - store_cond + - ph_meth + - cur_vegetation + - cur_vegetation_meth + - tot_org_carb + - tot_org_c_meth + - tot_nitro_content + - tot_nitro_cont_meth + - microbial_biomass + - micro_biomass_meth + - heavy_metals_meth + - tot_carb + - tot_phosphate + - sieving + - pool_dna_extracts + - misc_param + slot_usage: + adapters: + name: adapters + required: true + annot: + name: annot + recommended: true + assembly_name: + name: assembly_name + required: true + assembly_qual: + name: assembly_qual + assembly_software: + name: assembly_software + biotic_relationship: + name: biotic_relationship + recommended: true + chem_administration: + name: chem_administration + required: true + chimera_check: + name: chimera_check + required: true + climate_environment: + name: climate_environment + string_serialization: '{text};{period};{interval};{period}' + recommended: true + crop_rotation: + name: crop_rotation + string_serialization: '{boolean};Rn/{timestamp}/{period}' + recommended: true + cur_vegetation: + name: cur_vegetation + recommended: true + cur_vegetation_meth: + name: cur_vegetation_meth + recommended: true + depth: + name: depth + examples: + - value: 5 cm + recommended: true + drainage_class: + name: drainage_class + recommended: true + elev: + name: elev + required: false + recommended: false + enrichment_protocol: + name: enrichment_protocol + recommended: true + extreme_event: + name: extreme_event + recommended: true + fao_class: + name: fao_class + recommended: true + fire: + name: fire + recommended: true + flooding: + name: flooding + recommended: true + food_prod: + name: food_prod + required: false + recommended: false + food_product_type: + name: food_product_type + examples: + - value: delicatessen salad; FOODON:03316276 + required: false + recommended: false + food_source: + name: food_source + examples: + - value: red swamp crayfish; FOODON:03412231 + required: true + fungicide_regm: + name: fungicide_regm + string_serialization: '{text};{float} {unit};{period};{interval};{period}' + recommended: true + gaseous_environment: + name: gaseous_environment + string_serialization: '{text};{float} {unit};{period};{interval};{period}' + recommended: true + heavy_metals_meth: + name: heavy_metals_meth + string_serialization: '{PMID|DOI|URL}' + recommended: true + herbicide_regm: + name: herbicide_regm + string_serialization: '{text};{float} {unit};{period};{interval};{period}' + recommended: true + horizon_meth: + name: horizon_meth + recommended: true + host_age: + name: host_age + required: true + host_common_name: + name: host_common_name + required: true + host_disease_stat: + name: host_disease_stat + examples: + - value: downy mildew + recommended: true + host_genotype: + name: host_genotype + required: true + host_height: + name: host_height + required: true + host_length: + name: host_length + required: true + host_life_stage: + name: host_life_stage + required: true + host_phenotype: + name: host_phenotype + required: true + host_spec_range: + name: host_spec_range + required: true + host_symbiont: + name: host_symbiont + examples: + - value: Paragordius varius + host_taxid: + name: host_taxid + examples: + - value: '9606' + string_serialization: '{integer}' + required: true + host_tot_mass: + name: host_tot_mass + required: true + humidity: + name: humidity + examples: + - value: 30% relative humidity + recommended: true + isol_growth_condt: + name: isol_growth_condt + required: false + recommended: false + lib_layout: + name: lib_layout + recommended: true + lib_reads_seqd: + name: lib_reads_seqd + required: true + lib_screen: + name: lib_screen + required: true + lib_size: + name: lib_size + required: false + recommended: false + lib_vector: + name: lib_vector + required: true + library_prep_kit: + name: library_prep_kit + examples: + - value: llumina DNA Prep, (M) Tagmentation + local_class: + name: local_class + recommended: true + local_class_meth: + name: local_class_meth + recommended: true + micro_biomass_meth: + name: micro_biomass_meth + required: true + microbial_biomass: + name: microbial_biomass + required: true + mid: + name: mid + required: true + non_min_nutr_regm: + name: non_min_nutr_regm + string_serialization: '{text};{float} {unit};{period};{interval};{period}' + recommended: true + nucl_acid_amp: + name: nucl_acid_amp + required: true + nucl_acid_ext: + name: nucl_acid_ext + required: true + organism_count: + name: organism_count + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + recommended: true + oxy_stat_samp: + name: oxy_stat_samp + recommended: true + pathogenicity: + name: pathogenicity + required: true + pcr_cond: + name: pcr_cond + required: true + pcr_primers: + name: pcr_primers + required: true + perturbation: + name: perturbation + recommended: true + pesticide_regm: + name: pesticide_regm + string_serialization: '{text};{float} {unit};{period};{interval};{period}' + recommended: true + ph_meth: + name: ph_meth + recommended: true + ph_regm: + name: ph_regm + string_serialization: '{float};{period};{interval};{period}' + recommended: true + plant_growth_med: + name: plant_growth_med + examples: + - value: hydroponic plant culture media [EO:0007067] + plant_product: + name: plant_product + recommended: true + plant_struc: + name: plant_struc + recommended: true + pool_dna_extracts: + name: pool_dna_extracts + string_serialization: '{boolean};{float} {unit}' + required: true + prev_land_use_meth: + name: prev_land_use_meth + recommended: true + previous_land_use: + name: previous_land_use + recommended: true + profile_position: + name: profile_position + recommended: true + rel_location: + name: rel_location + recommended: true + salt_regm: + name: salt_regm + string_serialization: '{text};{float} {unit};{period};{interval};{period}' + recommended: true + samp_collect_device: + name: samp_collect_device + examples: + - value: biopsy, niskin bottle, push core + required: true + samp_collect_method: + name: samp_collect_method + examples: + - value: environmental swab sampling + required: false + recommended: false + samp_mat_process: + name: samp_mat_process + required: true + samp_pooling: + name: samp_pooling + recommended: true + samp_size: + name: samp_size + required: true + samp_store_dur: + name: samp_store_dur + required: true + samp_store_loc: + name: samp_store_loc + required: true + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: true + season_environment: + name: season_environment + string_serialization: '{text};{period};{interval};{period}' + recommended: true + season_precpt: + name: season_precpt + seq_quality_check: + name: seq_quality_check + required: false + recommended: false + sieving: + name: sieving + required: true + slope_aspect: + name: slope_aspect + recommended: true + slope_gradient: + name: slope_gradient + recommended: true + soil_conductivity: + name: soil_conductivity + description: Conductivity of some soil. + soil_cover: + name: soil_cover + recommended: true + soil_horizon: + name: soil_horizon + recommended: true + soil_pH: + name: soil_pH + description: pH of some soil. + soil_temp: + name: soil_temp + soil_type: + name: soil_type + string_serialization: '{text}' + required: true + soil_type_meth: + name: soil_type_meth + required: true + sop: + name: sop + required: false + recommended: false + source_mat_id: + name: source_mat_id + required: false + recommended: false + specific_host: + name: specific_host + required: true + standing_water_regm: + name: standing_water_regm + string_serialization: '{text};{period};{interval};{period}' + recommended: true + store_cond: + name: store_cond + required: true + target_gene: + name: target_gene + required: true + target_subfragment: + name: target_subfragment + required: true + temp: + name: temp + required: true + tillage: + name: tillage + recommended: true + tot_carb: + name: tot_carb + recommended: true + tot_nitro_cont_meth: + name: tot_nitro_cont_meth + recommended: true + tot_nitro_content: + name: tot_nitro_content + recommended: true + tot_org_c_meth: + name: tot_org_c_meth + recommended: true + tot_org_carb: + name: tot_org_carb + recommended: true + tot_phosphate: + name: tot_phosphate + recommended: true + trophic_level: + name: trophic_level + recommended: true + water_pH: + name: water_pH + description: The pH measurement of the sample, or liquid portion of sample, + or aqueous phase of the fluid. + water_temp_regm: + name: water_temp_regm + string_serialization: '{float} {unit};{period};{interval};{period}' + recommended: true + watering_regm: + name: watering_regm + string_serialization: '{float} {unit};{period};{interval};{period}' + recommended: true + class_uri: MIXS:0016018 + Air: + name: Air + description: air extension + title: air + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Extension + slots: + - samp_name + - project_name + - alt + - elev + - barometric_press + - carb_dioxide + - carb_monoxide + - chem_administration + - humidity + - methane + - organism_count + - oxygen + - oxy_stat_samp + - perturbation + - pollutants + - air_PM_concen + - salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - solar_irradiance + - temp + - ventilation_rate + - ventilation_type + - volatile_org_comp + - wind_direction + - wind_speed + - misc_param + slot_usage: + air_PM_concen: + name: air_PM_concen + alt: + name: alt + required: true + carb_dioxide: + name: carb_dioxide + required: false + recommended: false + chem_administration: + name: chem_administration + required: false + recommended: false + elev: + name: elev + recommended: true + humidity: + name: humidity + examples: + - value: 25 gram per cubic meter + required: false + recommended: false + methane: + name: methane + examples: + - value: 1800 parts per billion + organism_count: + name: organism_count + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + required: false + recommended: false + oxy_stat_samp: + name: oxy_stat_samp + required: false + recommended: false + perturbation: + name: perturbation + required: false + recommended: false + samp_store_dur: + name: samp_store_dur + required: false + recommended: false + samp_store_loc: + name: samp_store_loc + required: false + recommended: false + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: false + recommended: false + temp: + name: temp + required: false + recommended: false + ventilation_type: + name: ventilation_type + required: false + recommended: false + wind_direction: + name: wind_direction + examples: + - value: Northwest + wind_speed: + name: wind_speed + examples: + - value: 21 kilometer per hour + class_uri: MIXS:0016000 + BuiltEnvironment: + name: BuiltEnvironment + description: built environment extension + title: built environment + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Extension + slots: + - samp_name + - project_name + - surf_material + - surf_air_cont + - rel_air_humidity + - abs_air_humidity + - surf_humidity + - air_temp + - surf_temp + - surf_moisture_ph + - build_occup_type + - surf_moisture + - dew_point + - carb_dioxide + - ventilation_type + - organism_count + - indoor_space + - indoor_surf + - filter_type + - heat_cool_type + - substructure_type + - building_setting + - light_type + - samp_sort_meth + - space_typ_state + - typ_occup_density + - occup_samp + - occup_density_samp + - address + - adj_room + - aero_struc + - amount_light + - arch_struc + - avg_occup + - avg_dew_point + - avg_temp + - bathroom_count + - bedroom_count + - built_struc_age + - built_struc_set + - built_struc_type + - ceil_area + - ceil_cond + - ceil_finish_mat + - ceil_water_mold + - ceil_struc + - ceil_texture + - ceil_thermal_mass + - ceil_type + - cool_syst_id + - date_last_rain + - build_docs + - door_size + - door_cond + - door_direct + - door_loc + - door_mat + - door_move + - door_water_mold + - door_type + - door_comp_type + - door_type_metal + - door_type_wood + - drawings + - elevator + - escalator + - exp_duct + - exp_pipe + - ext_door + - fireplace_type + - floor_age + - floor_area + - floor_cond + - floor_count + - floor_finish_mat + - floor_water_mold + - floor_struc + - floor_thermal_mass + - freq_clean + - freq_cook + - furniture + - gender_restroom + - hall_count + - handidness + - heat_deliv_loc + - heat_sys_deliv_meth + - heat_system_id + - height_carper_fiber + - inside_lux + - int_wall_cond + - last_clean + - max_occup + - mech_struc + - number_plants + - number_pets + - number_resident + - occup_document + - ext_wall_orient + - ext_window_orient + - rel_humidity_out + - pres_animal_insect + - quad_pos + - rel_samp_loc + - room_air_exch_rate + - room_architec_elem + - room_condt + - room_count + - room_dim + - room_door_dist + - room_loc + - room_moist_dam_hist + - room_net_area + - room_occup + - room_samp_pos + - room_type + - room_vol + - room_window_count + - room_connected + - room_hallway + - room_door_share + - room_wall_share + - samp_weather + - samp_floor + - samp_room_id + - samp_time_out - season - - solar_irradiance - - crop_yield - - season_humidity - - humidity - - adjacent_environment - - chem_administration - - food_prod - - lot_number - - fertilizer_admin - - samp_store_temp - - food_trav_mode - - food_trav_vehic - - farm_equip_san - - farm_equip - - farm_equip_shared - - food_harvest_proc - - plant_struc - - host_dry_mass - - ances_data - - genetic_mod - - food_product_type - - food_source - - spikein_strain - - organism_count - - size_frac_low - - size_frac_up - - cult_isol_date - - samp_pooling - - root_med_macronutr - - root_med_carbon - - root_med_ph - - depth - - specific_host - - pathogenicity - - biotic_relationship - - water_temp_regm - - watering_regm - - standing_water_regm - - gaseous_environment - - fungicide_regm - - climate_environment - - herbicide_regm - - non_min_nutr_regm - - pesticide_regm - - ph_regm - - salt_regm - - season_environment - - temp - - perturbation - - isol_growth_condt - - samp_store_dur - - samp_store_loc - - samp_collect_device - - samp_mat_process - - host_age - - host_common_name - - host_genotype - - host_height - - host_subspecf_genlin - - host_length - - host_life_stage - - host_phenotype - - host_taxid - - host_tot_mass - - host_spec_range - - trophic_level - - plant_product - - samp_size - - oxy_stat_samp - - seq_meth - - samp_vol_we_dna_ext - - pcr_primers - - nucl_acid_ext - - nucl_acid_amp - - lib_size - - lib_reads_seqd - - lib_layout - - lib_vector - - lib_screen - - target_gene - - target_subfragment - - mid - - adapters - - pcr_cond - - seq_quality_check - - chimera_check - - assembly_name - - assembly_qual - - assembly_software - - annot - - associated_resource - - sop - - source_mat_id - - fao_class - - local_class - - local_class_meth - - soil_type - - soil_type_meth - - soil_horizon - - horizon_meth - - link_class_info - - previous_land_use - - prev_land_use_meth - - crop_rotation - - agrochem_addition - - tillage - - fire - - flooding - - extreme_event - - link_climate_info - - annual_temp - - season_temp - - annual_precpt - - season_precpt - - cur_land_use - - slope_gradient - - slope_aspect - - profile_position - - drainage_class - - store_cond - - ph_meth - - cur_vegetation - - cur_vegetation_meth - - tot_org_carb - - tot_org_c_meth - - tot_nitro_content - - tot_nitro_cont_meth - - microbial_biomass - - micro_biomass_meth - - heavy_metals_meth - - tot_carb - - tot_phosphate - - sieving - - pool_dna_extracts - - misc_param + - season_use + - shading_device_cond + - shading_device_loc + - shading_device_mat + - shad_dev_water_mold + - shading_device_type + - specific_humidity + - specific + - temp_out + - train_line + - train_stat_loc + - train_stop_loc + - vis_media + - wall_area + - wall_const_type + - wall_finish_mat + - wall_height + - wall_loc + - wall_water_mold + - wall_surf_treatment + - wall_texture + - wall_thermal_mass + - water_feat_size + - water_feat_type + - weekday + - window_size + - window_cond + - window_cover + - window_horiz_pos + - window_loc + - window_mat + - window_open_freq + - window_water_mold + - window_status + - window_type + - window_vert_pos slot_usage: - adapters: - name: adapters - required: true - annot: - name: annot - recommended: true - assembly_name: - name: assembly_name + air_temp: + name: air_temp + examples: + - value: 20 degree Celsius required: true - assembly_qual: - name: assembly_qual - assembly_software: - name: assembly_software - biotic_relationship: - name: biotic_relationship - recommended: true - chem_administration: - name: chem_administration + avg_occup: + name: avg_occup + examples: + - value: '2' + carb_dioxide: + name: carb_dioxide required: true - chimera_check: - name: chimera_check + freq_clean: + name: freq_clean + string_serialization: '[ Daily| Weekly| Monthly| Quarterly | Annually| other]' + indoor_surf: + name: indoor_surf required: true - climate_environment: - name: climate_environment - string_serialization: '{text};{period};{interval};{period}' - recommended: true - crop_rotation: - name: crop_rotation - string_serialization: '{boolean};Rn/{timestamp}/{period}' recommended: true - cur_vegetation: - name: cur_vegetation - recommended: true - cur_vegetation_meth: - name: cur_vegetation_meth - recommended: true - depth: - name: depth + organism_count: + name: organism_count examples: - - value: 5 cm - recommended: true - drainage_class: - name: drainage_class + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + required: true + surf_material: + name: surf_material + required: true recommended: true - elev: - name: elev - required: false - recommended: false + ventilation_type: + name: ventilation_type + required: true + class_uri: MIXS:0016001 + FoodAnimalAndAnimalFeed: + name: FoodAnimalAndAnimalFeed + description: food-animal and animal feed extension + title: food-animal and animal feed + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Extension + slots: + - samp_name + - project_name + - lat_lon + - geo_loc_name + - collection_date + - seq_meth + - samp_size + - samp_collect_device + - experimental_factor + - nucl_acid_ext + - organism_count + - spikein_count + - samp_store_temp + - samp_store_dur + - samp_vol_we_dna_ext + - pool_dna_extracts + - temp + - samp_store_loc + - samp_transport_cont + - perturbation + - coll_site_geo_feat + - food_origin + - food_prod + - food_product_type + - food_source + - IFSAC_category + - intended_consumer + - samp_purpose + - animal_am + - animal_am_dur + - animal_am_freq + - animal_am_route + - animal_am_use + - animal_body_cond + - animal_diet + - animal_feed_equip + - animal_group_size + - animal_housing + - animal_sex + - bacterial_density + - cons_food_stor_dur + - cons_food_stor_temp + - cons_purch_date + - cons_qty_purchased + - cult_isol_date + - cult_result + - cult_result_org + - cult_target + - enrichment_protocol + - food_additive + - food_contact_surf + - food_contain_wrap + - food_cooking_proc + - food_dis_point + - food_dis_point_city + - food_ingredient + - food_pack_capacity + - food_pack_integrity + - food_pack_medium + - food_preserv_proc + - food_prior_contact + - food_prod_synonym + - food_product_qual + - food_quality_date + - food_source_age + - food_trace_list + - food_trav_mode + - food_trav_vehic + - food_treat_proc + - HACCP_term + - library_prep_kit + - lot_number + - microb_cult_med + - part_plant_animal + - repository_name + - samp_collect_method + - samp_pooling + - samp_rep_biol + - samp_rep_tech + - samp_source_mat_cat + - samp_stor_device + - samp_stor_media + - samp_transport_dur + - samp_transport_temp + - sequencing_kit + - sequencing_location + - serovar_or_serotype + - spikein_AMR + - spikein_antibiotic + - spikein_growth_med + - spikein_metal + - spikein_org + - spikein_serovar + - spikein_strain + - study_design + - study_inc_dur + - study_inc_temp + - study_timecourse + - study_tmnt + - timepoint + - misc_param + slot_usage: enrichment_protocol: name: enrichment_protocol - recommended: true - extreme_event: - name: extreme_event - recommended: true - fao_class: - name: fao_class - recommended: true - fire: - name: fire - recommended: true - flooding: - name: flooding - recommended: true - food_prod: - name: food_prod required: false recommended: false - food_product_type: - name: food_product_type - examples: - - value: delicatessen salad; FOODON:03316276 + experimental_factor: + name: experimental_factor required: false recommended: false - food_source: - name: food_source - examples: - - value: red swamp crayfish; FOODON:03412231 - required: true - fungicide_regm: - name: fungicide_regm - string_serialization: '{text};{float} {unit};{period};{interval};{period}' - recommended: true - gaseous_environment: - name: gaseous_environment - string_serialization: '{text};{float} {unit};{period};{interval};{period}' - recommended: true - heavy_metals_meth: - name: heavy_metals_meth - string_serialization: '{PMID|DOI|URL}' - recommended: true - herbicide_regm: - name: herbicide_regm - string_serialization: '{text};{float} {unit};{period};{interval};{period}' - recommended: true - horizon_meth: - name: horizon_meth - recommended: true - host_age: - name: host_age - required: true - host_common_name: - name: host_common_name - required: true - host_disease_stat: - name: host_disease_stat - examples: - - value: downy mildew - recommended: true - host_genotype: - name: host_genotype - required: true - host_height: - name: host_height - required: true - host_length: - name: host_length - required: true - host_life_stage: - name: host_life_stage - required: true - host_phenotype: - name: host_phenotype - required: true - host_spec_range: - name: host_spec_range + food_contact_surf: + name: food_contact_surf + required: false + recommended: false + food_origin: + name: food_origin required: true - host_symbiont: - name: host_symbiont - examples: - - value: Paragordius varius - host_taxid: - name: host_taxid + food_pack_medium: + name: food_pack_medium examples: - - value: '9606' - string_serialization: '{integer}' - required: true - host_tot_mass: - name: host_tot_mass + - value: packed in fruit juice [FOODON:03480039] + food_prod: + name: food_prod required: true - humidity: - name: humidity - examples: - - value: 30% relative humidity - recommended: true - isol_growth_condt: - name: isol_growth_condt + food_product_qual: + name: food_product_qual required: false recommended: false - lib_layout: - name: lib_layout - recommended: true - lib_reads_seqd: - name: lib_reads_seqd - required: true - lib_screen: - name: lib_screen + food_product_type: + name: food_product_type + examples: + - value: shrimp (peeled, deep-frozen) [FOODON:03317171] required: true - lib_size: - name: lib_size + food_source: + name: food_source + examples: + - value: giant tiger prawn [FOODON:03412612] required: false recommended: false - lib_vector: - name: lib_vector + intended_consumer: + name: intended_consumer required: true library_prep_kit: name: library_prep_kit examples: - - value: llumina DNA Prep, (M) Tagmentation - local_class: - name: local_class - recommended: true - local_class_meth: - name: local_class_meth - recommended: true - micro_biomass_meth: - name: micro_biomass_meth - required: true - microbial_biomass: - name: microbial_biomass - required: true - mid: - name: mid - required: true - non_min_nutr_regm: - name: non_min_nutr_regm - string_serialization: '{text};{float} {unit};{period};{interval};{period}' - recommended: true - nucl_acid_amp: - name: nucl_acid_amp - required: true + - value: Illumina DNA Prep nucl_acid_ext: name: nucl_acid_ext - required: true + required: false + recommended: false organism_count: name: organism_count examples: - - value: total prokaryotes;3.5e7 cells per milliliter;qPCR - recommended: true - oxy_stat_samp: - name: oxy_stat_samp - recommended: true - pathogenicity: - name: pathogenicity - required: true - pcr_cond: - name: pcr_cond - required: true - pcr_primers: - name: pcr_primers - required: true + - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR + required: false + recommended: false perturbation: name: perturbation - recommended: true - pesticide_regm: - name: pesticide_regm - string_serialization: '{text};{float} {unit};{period};{interval};{period}' - recommended: true - ph_meth: - name: ph_meth - recommended: true - ph_regm: - name: ph_regm - string_serialization: '{float};{period};{interval};{period}' - recommended: true - plant_growth_med: - name: plant_growth_med - examples: - - value: hydroponic plant culture media [EO:0007067] - plant_product: - name: plant_product - recommended: true - plant_struc: - name: plant_struc - recommended: true + required: false + recommended: false pool_dna_extracts: name: pool_dna_extracts - string_serialization: '{boolean};{float} {unit}' - required: true - prev_land_use_meth: - name: prev_land_use_meth - recommended: true - previous_land_use: - name: previous_land_use - recommended: true - profile_position: - name: profile_position - recommended: true - rel_location: - name: rel_location - recommended: true - salt_regm: - name: salt_regm - string_serialization: '{text};{float} {unit};{period};{interval};{period}' - recommended: true + string_serialization: '{boolean},{integer}' + required: false + recommended: false samp_collect_device: name: samp_collect_device examples: - - value: biopsy, niskin bottle, push core - required: true + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + required: false + recommended: false samp_collect_method: name: samp_collect_method examples: - value: environmental swab sampling required: false recommended: false - samp_mat_process: - name: samp_mat_process - required: true samp_pooling: name: samp_pooling - recommended: true + required: false + recommended: false + samp_purpose: + name: samp_purpose + required: true samp_size: name: samp_size - required: true + required: false + recommended: false + samp_source_mat_cat: + name: samp_source_mat_cat + required: false + recommended: false + samp_stor_device: + name: samp_stor_device + required: false + recommended: false + samp_stor_media: + name: samp_stor_media + required: false + recommended: false samp_store_dur: name: samp_store_dur - required: true - samp_store_loc: - name: samp_store_loc - required: true - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: true - season_environment: - name: season_environment - string_serialization: '{text};{period};{interval};{period}' - recommended: true - season_precpt: - name: season_precpt - seq_quality_check: - name: seq_quality_check required: false recommended: false - sieving: - name: sieving - required: true - slope_aspect: - name: slope_aspect - recommended: true - slope_gradient: - name: slope_gradient - recommended: true - soil_conductivity: - name: soil_conductivity - description: Conductivity of some soil. - soil_cover: - name: soil_cover - recommended: true - soil_horizon: - name: soil_horizon - recommended: true - soil_pH: - name: soil_pH - description: pH of some soil. - soil_temp: - name: soil_temp - soil_type: - name: soil_type - string_serialization: '{text}' - required: true - soil_type_meth: - name: soil_type_meth - required: true - sop: - name: sop + samp_store_loc: + name: samp_store_loc required: false recommended: false - source_mat_id: - name: source_mat_id + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext required: false recommended: false - specific_host: - name: specific_host - required: true - standing_water_regm: - name: standing_water_regm - string_serialization: '{text};{period};{interval};{period}' - recommended: true - store_cond: - name: store_cond - required: true - target_gene: - name: target_gene - required: true - target_subfragment: - name: target_subfragment - required: true temp: name: temp - required: true - tillage: - name: tillage - recommended: true - tot_carb: - name: tot_carb - recommended: true - tot_nitro_cont_meth: - name: tot_nitro_cont_meth - recommended: true - tot_nitro_content: - name: tot_nitro_content - recommended: true - tot_org_c_meth: - name: tot_org_c_meth - recommended: true - tot_org_carb: - name: tot_org_carb - recommended: true - tot_phosphate: - name: tot_phosphate - recommended: true - trophic_level: - name: trophic_level - recommended: true - water_pH: - name: water_pH - description: The pH measurement of the sample, or liquid portion of sample, - or aqueous phase of the fluid. - water_temp_regm: - name: water_temp_regm - string_serialization: '{float} {unit};{period};{interval};{period}' - recommended: true - watering_regm: - name: watering_regm - string_serialization: '{float} {unit};{period};{interval};{period}' - recommended: true - class_uri: MIXS:0016018 - Air: - name: Air - description: air extension - title: air + required: false + recommended: false + class_uri: MIXS:0016019 + FoodFarmEnvironment: + name: FoodFarmEnvironment + description: food-farm environment extension + title: food-farm environment from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: - samp_name - project_name - - alt - - elev - - barometric_press - - carb_dioxide - - carb_monoxide - - chem_administration + - lat_lon + - geo_loc_name + - collection_date + - seq_meth + - samp_size + - samp_collect_device + - nucl_acid_ext - humidity - - methane - organism_count - - oxygen - - oxy_stat_samp - - perturbation - - pollutants - - air_PM_concen - - salinity - - samp_store_dur - - samp_store_loc + - spikein_count - samp_store_temp - - samp_vol_we_dna_ext - solar_irradiance - - temp - ventilation_rate + - samp_store_dur + - wind_speed + - salinity + - samp_vol_we_dna_ext + - previous_land_use + - crop_rotation + - soil_type_meth + - tot_org_c_meth + - tot_nitro_cont_meth + - host_age + - host_dry_mass + - host_height + - host_length + - host_tot_mass + - root_med_carbon + - root_med_macronutr + - root_med_micronutr + - depth + - season_temp + - season_precpt + - tot_org_carb + - tot_nitro_content + - conduc + - turbidity + - size_frac_low + - size_frac_up + - temp - ventilation_type - - volatile_org_comp - wind_direction - - wind_speed + - genetic_mod + - host_phenotype + - ph + - ances_data + - biotic_regm + - chem_administration + - growth_habit + - host_disease_stat + - host_genotype + - host_taxid + - mechanical_damage + - perturbation + - root_cond + - root_med_ph + - tillage + - ph_meth + - growth_medium + - season + - food_product_type + - samp_type + - farm_water_source + - plant_water_method + - air_PM_concen + - animal_feed_equip + - animal_intrusion + - anim_water_method + - crop_yield + - cult_result + - cult_result_org + - cult_target + - plant_part_maturity + - adjacent_environment + - water_source_adjac + - farm_equip_shared + - farm_equip_san + - farm_equip_san_freq + - farm_equip + - fertilizer_admin + - fertilizer_date + - animal_group_size + - animal_diet + - food_contact_surf + - food_contain_wrap + - food_harvest_proc + - food_pack_medium + - food_preserv_proc + - food_prod_char + - prod_label_claims + - food_trav_mode + - food_trav_vehic + - food_source + - food_treat_proc + - extr_weather_event + - date_extr_weath + - host_subspecf_genlin + - intended_consumer + - library_prep_kit + - air_flow_impede + - lot_number + - season_humidity + - part_plant_animal + - plant_growth_med + - plant_reprod_crop + - samp_purpose + - repository_name + - samp_pooling + - samp_source_mat_cat + - sequencing_kit + - sequencing_location + - serovar_or_serotype + - soil_conductivity + - soil_cover + - soil_pH + - rel_location + - soil_porosity + - soil_temp + - soil_texture_class + - soil_texture_meth + - soil_type + - spikein_org + - spikein_serovar + - spikein_growth_med + - spikein_strain + - spikein_antibiotic + - spikein_metal + - timepoint + - water_frequency + - water_pH + - water_source_shared + - enrichment_protocol + - food_quality_date + - IFSAC_category + - animal_housing + - cult_isol_date + - food_clean_proc - misc_param slot_usage: air_PM_concen: name: air_PM_concen - alt: - name: alt + biotic_regm: + name: biotic_regm required: true - carb_dioxide: - name: carb_dioxide - required: false - recommended: false chem_administration: name: chem_administration + required: true + crop_rotation: + name: crop_rotation + string_serialization: '{boolean};{Rn/start_time/end_time/duration}' required: false recommended: false - elev: - name: elev + depth: + name: depth + examples: + - value: 10 meter + required: true + enrichment_protocol: + name: enrichment_protocol + required: false + recommended: false + food_contact_surf: + name: food_contact_surf + required: false + recommended: false + food_pack_medium: + name: food_pack_medium + examples: + - value: vacuum-packed [FOODON:03480027] + food_product_type: + name: food_product_type + examples: + - value: shrimp (peeled, deep-frozen) [FOODON:03317171] + required: true + food_source: + name: food_source + examples: + - value: giant tiger prawn [FOODON:03412612] + required: false + recommended: false + host_age: + name: host_age + examples: + - value: 10 days + required: false + recommended: false + host_disease_stat: + name: host_disease_stat + examples: + - value: downy mildew recommended: true + host_genotype: + name: host_genotype + examples: + - value: Ts + required: false + recommended: false + host_height: + name: host_height + examples: + - value: 1 meter + required: false + recommended: false + host_length: + name: host_length + required: false + recommended: false + host_phenotype: + name: host_phenotype + examples: + - value: seed pod; green [PATO:0000320] + required: false + recommended: false + host_taxid: + name: host_taxid + examples: + - value: '4530' + string_serialization: '{NCBI taxid}' + required: false + recommended: false + host_tot_mass: + name: host_tot_mass + examples: + - value: 2500 gram + required: false + recommended: false humidity: name: humidity examples: - - value: 25 gram per cubic meter + - value: 30% relative humidity + required: false + recommended: false + intended_consumer: + name: intended_consumer + required: false + recommended: false + library_prep_kit: + name: library_prep_kit + examples: + - value: Illumina DNA Prep + nucl_acid_ext: + name: nucl_acid_ext + required: false + recommended: false + organism_count: + name: organism_count + examples: + - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR + required: false + recommended: false + perturbation: + name: perturbation + required: false + recommended: false + ph: + name: ph required: false recommended: false - methane: - name: methane - examples: - - value: 1800 parts per billion - organism_count: - name: organism_count + ph_meth: + name: ph_meth + required: false + recommended: false + plant_growth_med: + name: plant_growth_med examples: - - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + - value: soil + previous_land_use: + name: previous_land_use required: false recommended: false - oxy_stat_samp: - name: oxy_stat_samp + rel_location: + name: rel_location required: false recommended: false - perturbation: - name: perturbation + samp_collect_device: + name: samp_collect_device + examples: + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] required: false recommended: false - samp_store_dur: - name: samp_store_dur + samp_pooling: + name: samp_pooling required: false recommended: false - samp_store_loc: - name: samp_store_loc + samp_purpose: + name: samp_purpose required: false recommended: false - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext + samp_size: + name: samp_size required: false recommended: false - temp: - name: temp + samp_source_mat_cat: + name: samp_source_mat_cat required: false recommended: false - ventilation_type: - name: ventilation_type + samp_store_dur: + name: samp_store_dur required: false recommended: false - wind_direction: - name: wind_direction - examples: - - value: Northwest - wind_speed: - name: wind_speed - examples: - - value: 21 kilometer per hour - class_uri: MIXS:0016000 - BuiltEnvironment: - name: BuiltEnvironment - description: built environment extension - title: built environment - from_schema: https://w3id.org/mixs-6-2-rc - is_a: Extension - slots: - - samp_name - - project_name - - surf_material - - surf_air_cont - - rel_air_humidity - - abs_air_humidity - - surf_humidity - - air_temp - - surf_temp - - surf_moisture_ph - - build_occup_type - - surf_moisture - - dew_point - - carb_dioxide - - ventilation_type - - organism_count - - indoor_space - - indoor_surf - - filter_type - - heat_cool_type - - substructure_type - - building_setting - - light_type - - samp_sort_meth - - space_typ_state - - typ_occup_density - - occup_samp - - occup_density_samp - - address - - adj_room - - aero_struc - - amount_light - - arch_struc - - avg_occup - - avg_dew_point - - avg_temp - - bathroom_count - - bedroom_count - - built_struc_age - - built_struc_set - - built_struc_type - - ceil_area - - ceil_cond - - ceil_finish_mat - - ceil_water_mold - - ceil_struc - - ceil_texture - - ceil_thermal_mass - - ceil_type - - cool_syst_id - - date_last_rain - - build_docs - - door_size - - door_cond - - door_direct - - door_loc - - door_mat - - door_move - - door_water_mold - - door_type - - door_comp_type - - door_type_metal - - door_type_wood - - drawings - - elevator - - escalator - - exp_duct - - exp_pipe - - ext_door - - fireplace_type - - floor_age - - floor_area - - floor_cond - - floor_count - - floor_finish_mat - - floor_water_mold - - floor_struc - - floor_thermal_mass - - freq_clean - - freq_cook - - furniture - - gender_restroom - - hall_count - - handidness - - heat_deliv_loc - - heat_sys_deliv_meth - - heat_system_id - - height_carper_fiber - - inside_lux - - int_wall_cond - - last_clean - - max_occup - - mech_struc - - number_plants - - number_pets - - number_resident - - occup_document - - ext_wall_orient - - ext_window_orient - - rel_humidity_out - - pres_animal_insect - - quad_pos - - rel_samp_loc - - room_air_exch_rate - - room_architec_elem - - room_condt - - room_count - - room_dim - - room_door_dist - - room_loc - - room_moist_dam_hist - - room_net_area - - room_occup - - room_samp_pos - - room_type - - room_vol - - room_window_count - - room_connected - - room_hallway - - room_door_share - - room_wall_share - - samp_weather - - samp_floor - - samp_room_id - - samp_time_out - - season - - season_use - - shading_device_cond - - shading_device_loc - - shading_device_mat - - shad_dev_water_mold - - shading_device_type - - specific_humidity - - specific - - temp_out - - train_line - - train_stat_loc - - train_stop_loc - - vis_media - - wall_area - - wall_const_type - - wall_finish_mat - - wall_height - - wall_loc - - wall_water_mold - - wall_surf_treatment - - wall_texture - - wall_thermal_mass - - water_feat_size - - water_feat_type - - weekday - - window_size - - window_cond - - window_cover - - window_horiz_pos - - window_loc - - window_mat - - window_open_freq - - window_water_mold - - window_status - - window_type - - window_vert_pos - slot_usage: - air_temp: - name: air_temp - examples: - - value: 20 degree Celsius - required: true - avg_occup: - name: avg_occup - examples: - - value: '2' - carb_dioxide: - name: carb_dioxide - required: true - freq_clean: - name: freq_clean - string_serialization: '[ Daily| Weekly| Monthly| Quarterly | Annually| other]' - indoor_surf: - name: indoor_surf - required: true - recommended: true - organism_count: - name: organism_count - examples: - - value: total prokaryotes;3.5e7 cells per milliliter;qPCR - required: true - surf_material: - name: surf_material - required: true - recommended: true + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: false + recommended: false + season_precpt: + name: season_precpt + soil_conductivity: + name: soil_conductivity + description: Conductivity of soil at time of sampling. + soil_cover: + name: soil_cover + required: false + recommended: false + soil_pH: + name: soil_pH + description: The pH of soil at time of sampling. + soil_temp: + name: soil_temp + soil_type: + name: soil_type + string_serialization: '{termLabel} [{termID}]' + required: false + recommended: false + soil_type_meth: + name: soil_type_meth + required: false + recommended: false + temp: + name: temp + required: false + recommended: false + tillage: + name: tillage + required: false + recommended: false + tot_nitro_cont_meth: + name: tot_nitro_cont_meth + required: false + recommended: false + tot_nitro_content: + name: tot_nitro_content + required: false + recommended: false + tot_org_c_meth: + name: tot_org_c_meth + required: false + recommended: false + tot_org_carb: + name: tot_org_carb + required: false + recommended: false + turbidity: + name: turbidity ventilation_type: name: ventilation_type - required: true - class_uri: MIXS:0016001 - FoodAnimalAndAnimalFeed: - name: FoodAnimalAndAnimalFeed - description: food-animal and animal feed extension - title: food-animal and animal feed + required: false + recommended: false + water_pH: + name: water_pH + description: pH measurement of the sample, or liquid portion of sample, or + aqueous phase of the fluid. + wind_direction: + name: wind_direction + examples: + - value: 0 degrees; Northwest + wind_speed: + name: wind_speed + examples: + - value: 1.6 kilometers per hour + class_uri: MIXS:0016020 + FoodFoodProductionFacility: + name: FoodFoodProductionFacility + description: food-food production facility extension + title: food-food production facility from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: @@ -21010,97 +24433,107 @@ classes: - experimental_factor - nucl_acid_ext - organism_count - - spikein_count - samp_store_temp - samp_store_dur + - air_temp + - room_dim + - freq_clean + - samp_room_id - samp_vol_we_dna_ext - pool_dna_extracts - - temp - samp_store_loc - - samp_transport_cont - - perturbation + - surf_material + - indoor_surf + - avg_occup + - samp_floor + - genetic_mod - coll_site_geo_feat - - food_origin - - food_prod + - samp_source_mat_cat + - samp_type + - samp_stor_media + - samp_stor_device - food_product_type - - food_source - IFSAC_category - - intended_consumer - - samp_purpose - - animal_am - - animal_am_dur - - animal_am_freq - - animal_am_route - - animal_am_use - - animal_body_cond - - animal_diet - - animal_feed_equip - - animal_group_size - - animal_housing - - animal_sex - - bacterial_density - - cons_food_stor_dur - - cons_food_stor_temp - - cons_purch_date - - cons_qty_purchased - - cult_isol_date - - cult_result - - cult_result_org - - cult_target - - enrichment_protocol - - food_additive - - food_contact_surf - - food_contain_wrap - - food_cooking_proc - - food_dis_point - - food_dis_point_city - - food_ingredient - - food_pack_capacity - - food_pack_integrity - - food_pack_medium - - food_preserv_proc - - food_prior_contact - - food_prod_synonym - food_product_qual - - food_quality_date - - food_source_age - - food_trace_list + - food_contact_surf + - facility_type - food_trav_mode - food_trav_vehic - - food_treat_proc - - HACCP_term - - library_prep_kit + - samp_transport_dur + - samp_transport_temp + - samp_collect_method + - num_samp_collect - lot_number + - hygienic_area + - env_monitoring_zone + - area_samp_size + - samp_surf_moisture + - samp_loc_condition + - biocide_used + - ster_meth_samp_room + - enrichment_protocol + - cult_target - microb_cult_med - - part_plant_animal - - repository_name - - samp_collect_method + - timepoint + - bacterial_density + - cult_isol_date + - cult_result + - cult_result_org + - subspecf_gen_lin - samp_pooling - - samp_rep_biol + - samp_purpose - samp_rep_tech - - samp_source_mat_cat - - samp_stor_device - - samp_stor_media - - samp_transport_dur - - samp_transport_temp + - samp_rep_biol + - samp_transport_cont + - study_design + - nucl_acid_ext_kit + - library_prep_kit - sequencing_kit - sequencing_location - - serovar_or_serotype - - spikein_AMR - - spikein_antibiotic - - spikein_growth_med - - spikein_metal - - spikein_org - - spikein_serovar - - spikein_strain - - study_design - - study_inc_dur - study_inc_temp + - study_inc_dur - study_timecourse - study_tmnt - - timepoint + - food_source + - food_dis_point + - food_dis_point_city + - food_origin + - food_prod_synonym + - food_additive + - food_trace_list + - part_plant_animal + - food_ingredient + - spec_intended_cons + - HACCP_term + - dietary_claim_use + - food_allergen_label + - food_prod_char + - prod_label_claims + - food_name_status + - food_preserv_proc + - food_cooking_proc + - food_treat_proc + - food_contain_wrap + - food_pack_capacity + - food_pack_medium + - food_prior_contact + - food_prod + - food_quality_date + - repository_name + - intended_consumer + - food_pack_integrity - misc_param slot_usage: + air_temp: + name: air_temp + examples: + - value: 4 degree Celsius + required: false + recommended: false + avg_occup: + name: avg_occup + examples: + - value: '6' enrichment_protocol: name: enrichment_protocol required: false @@ -21111,22 +24544,22 @@ classes: recommended: false food_contact_surf: name: food_contact_surf - required: false - recommended: false + required: true food_origin: name: food_origin - required: true + required: false + recommended: false food_pack_medium: name: food_pack_medium examples: - - value: packed in fruit juice [FOODON:03480039] + - value: vacuum-packed [FOODON:03480027] food_prod: name: food_prod - required: true - food_product_qual: - name: food_product_qual required: false recommended: false + food_product_qual: + name: food_product_qual + required: true food_product_type: name: food_product_type examples: @@ -21138,9 +24571,17 @@ classes: - value: giant tiger prawn [FOODON:03412612] required: false recommended: false + freq_clean: + name: freq_clean + string_serialization: '{text}' + indoor_surf: + name: indoor_surf + required: false + recommended: false intended_consumer: name: intended_consumer - required: true + required: false + recommended: false library_prep_kit: name: library_prep_kit examples: @@ -21150,13 +24591,9 @@ classes: required: false recommended: false organism_count: - name: organism_count - examples: - - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR - required: false - recommended: false - perturbation: - name: perturbation + name: organism_count + examples: + - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR required: false recommended: false pool_dna_extracts: @@ -21167,7 +24604,7 @@ classes: samp_collect_device: name: samp_collect_device examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + - value: biopsy, niskin bottle, push core required: false recommended: false samp_collect_method: @@ -21182,23 +24619,21 @@ classes: recommended: false samp_purpose: name: samp_purpose - required: true + required: false + recommended: false samp_size: name: samp_size required: false recommended: false samp_source_mat_cat: name: samp_source_mat_cat - required: false - recommended: false + required: true samp_stor_device: name: samp_stor_device - required: false - recommended: false + required: true samp_stor_media: name: samp_stor_media - required: false - recommended: false + required: true samp_store_dur: name: samp_store_dur required: false @@ -21211,15 +24646,17 @@ classes: name: samp_vol_we_dna_ext required: false recommended: false - temp: - name: temp + subspecf_gen_lin: + name: subspecf_gen_lin + surf_material: + name: surf_material required: false recommended: false - class_uri: MIXS:0016019 - FoodFarmEnvironment: - name: FoodFarmEnvironment - description: food-farm environment extension - title: food-farm environment + class_uri: MIXS:0016021 + FoodHumanFoods: + name: FoodHumanFoods + description: food-human foods extension + title: food-human foods from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: @@ -21231,230 +24668,145 @@ classes: - seq_meth - samp_size - samp_collect_device + - experimental_factor - nucl_acid_ext - - humidity - organism_count - spikein_count - samp_store_temp - - solar_irradiance - - ventilation_rate - samp_store_dur - - wind_speed - - salinity - samp_vol_we_dna_ext - - previous_land_use - - crop_rotation - - soil_type_meth - - tot_org_c_meth - - tot_nitro_cont_meth - - host_age - - host_dry_mass - - host_height - - host_length - - host_tot_mass - - root_med_carbon - - root_med_macronutr - - root_med_micronutr - - depth - - season_temp - - season_precpt - - tot_org_carb - - tot_nitro_content - - conduc - - turbidity - - size_frac_low - - size_frac_up + - pool_dna_extracts - temp - - ventilation_type - - wind_direction + - samp_store_loc - genetic_mod - - host_phenotype - - ph - - ances_data - - biotic_regm - - chem_administration - - growth_habit - - host_disease_stat - - host_genotype - - host_taxid - - mechanical_damage - perturbation - - root_cond - - root_med_ph - - tillage - - ph_meth - - growth_medium - - season + - coll_site_geo_feat - food_product_type - - samp_type - - farm_water_source - - plant_water_method - - air_PM_concen - - animal_feed_equip - - animal_intrusion - - anim_water_method - - crop_yield + - IFSAC_category + - ferm_chem_add + - ferm_chem_add_perc + - ferm_headspace_oxy + - ferm_medium + - ferm_pH + - ferm_rel_humidity + - ferm_temp + - ferm_time + - ferm_vessel + - bacterial_density + - cons_food_stor_dur + - cons_food_stor_temp + - cons_purch_date + - cons_qty_purchased + - cult_isol_date - cult_result - cult_result_org - cult_target - - plant_part_maturity - - adjacent_environment - - water_source_adjac - - farm_equip_shared - - farm_equip_san - - farm_equip_san_freq - - farm_equip - - fertilizer_admin - - fertilizer_date - - animal_group_size - - animal_diet + - dietary_claim_use + - enrichment_protocol + - food_additive + - food_allergen_label - food_contact_surf - food_contain_wrap - - food_harvest_proc + - food_cooking_proc + - food_dis_point + - food_ingredient + - food_name_status + - food_origin + - food_pack_capacity + - food_pack_integrity - food_pack_medium - food_preserv_proc - - food_prod_char - - prod_label_claims + - food_prior_contact + - food_prod + - food_prod_synonym + - food_product_qual + - food_quality_date + - food_source + - food_trace_list - food_trav_mode - food_trav_vehic - - food_source - food_treat_proc - - extr_weather_event - - date_extr_weath - - host_subspecf_genlin + - HACCP_term - intended_consumer - library_prep_kit - - air_flow_impede - lot_number - - season_humidity + - microb_cult_med + - microb_start + - microb_start_count + - microb_start_inoc + - microb_start_prep + - microb_start_source + - microb_start_taxID + - nucl_acid_ext_kit + - num_samp_collect - part_plant_animal - - plant_growth_med - - plant_reprod_crop - - samp_purpose - repository_name + - samp_collect_method - samp_pooling + - samp_rep_biol + - samp_rep_tech - samp_source_mat_cat + - samp_stor_device + - samp_stor_media + - samp_transport_cont + - samp_transport_dur + - samp_transport_temp + - samp_purpose - sequencing_kit - sequencing_location - serovar_or_serotype - - soil_conductivity - - soil_cover - - soil_pH - - rel_location - - soil_porosity - - soil_temp - - soil_texture_class - - soil_texture_meth - - soil_type + - spikein_AMR + - spikein_antibiotic + - spikein_growth_med + - spikein_metal - spikein_org - spikein_serovar - - spikein_growth_med - spikein_strain - - spikein_antibiotic - - spikein_metal + - study_design + - study_inc_dur + - study_inc_temp + - study_timecourse + - study_tmnt - timepoint - - water_frequency - - water_pH - - water_source_shared - - enrichment_protocol - - food_quality_date - - IFSAC_category - - animal_housing - - cult_isol_date - - food_clean_proc - misc_param slot_usage: - air_PM_concen: - name: air_PM_concen - biotic_regm: - name: biotic_regm - required: true - chem_administration: - name: chem_administration - required: true - crop_rotation: - name: crop_rotation - string_serialization: '{boolean};{Rn/start_time/end_time/duration}' - required: false - recommended: false - depth: - name: depth - examples: - - value: 10 meter - required: true enrichment_protocol: name: enrichment_protocol required: false recommended: false - food_contact_surf: - name: food_contact_surf - required: false - recommended: false - food_pack_medium: - name: food_pack_medium - examples: - - value: vacuum-packed [FOODON:03480027] - food_product_type: - name: food_product_type - examples: - - value: shrimp (peeled, deep-frozen) [FOODON:03317171] - required: true - food_source: - name: food_source - examples: - - value: giant tiger prawn [FOODON:03412612] - required: false - recommended: false - host_age: - name: host_age - examples: - - value: 10 days - required: false - recommended: false - host_disease_stat: - name: host_disease_stat - examples: - - value: downy mildew - recommended: true - host_genotype: - name: host_genotype - examples: - - value: Ts - required: false - recommended: false - host_height: - name: host_height - examples: - - value: 1 meter + experimental_factor: + name: experimental_factor required: false recommended: false - host_length: - name: host_length + food_contact_surf: + name: food_contact_surf required: false recommended: false - host_phenotype: - name: host_phenotype - examples: - - value: seed pod; green [PATO:0000320] + food_origin: + name: food_origin required: false recommended: false - host_taxid: - name: host_taxid + food_pack_medium: + name: food_pack_medium examples: - - value: '4530' - string_serialization: '{NCBI taxid}' + - value: vacuum-packed[FOODON:03480027] + food_prod: + name: food_prod required: false recommended: false - host_tot_mass: - name: host_tot_mass - examples: - - value: 2500 gram + food_product_qual: + name: food_product_qual required: false recommended: false - humidity: - name: humidity + food_product_type: + name: food_product_type examples: - - value: 30% relative humidity + - value: shrimp (peeled, deep-frozen) [FOODON:03317171] + required: true + food_source: + name: food_source + examples: + - value: giant tiger prawn [FOODON:03412612] required: false recommended: false intended_consumer: @@ -21479,24 +24831,9 @@ classes: name: perturbation required: false recommended: false - ph: - name: ph - required: false - recommended: false - ph_meth: - name: ph_meth - required: false - recommended: false - plant_growth_med: - name: plant_growth_med - examples: - - value: soil - previous_land_use: - name: previous_land_use - required: false - recommended: false - rel_location: - name: rel_location + pool_dna_extracts: + name: pool_dna_extracts + string_serialization: '{boolean},{integer}' required: false recommended: false samp_collect_device: @@ -21505,6 +24842,12 @@ classes: - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] required: false recommended: false + samp_collect_method: + name: samp_collect_method + examples: + - value: environmental swab sampling + required: false + recommended: false samp_pooling: name: samp_pooling required: false @@ -21521,299 +24864,379 @@ classes: name: samp_source_mat_cat required: false recommended: false + samp_stor_device: + name: samp_stor_device + required: false + recommended: false + samp_stor_media: + name: samp_stor_media + required: false + recommended: false samp_store_dur: name: samp_store_dur required: false recommended: false + samp_store_loc: + name: samp_store_loc + required: false + recommended: false samp_vol_we_dna_ext: name: samp_vol_we_dna_ext required: false recommended: false - season_precpt: - name: season_precpt - soil_conductivity: - name: soil_conductivity - description: Conductivity of soil at time of sampling. - soil_cover: - name: soil_cover + temp: + name: temp required: false recommended: false - soil_pH: - name: soil_pH - description: The pH of soil at time of sampling. - soil_temp: - name: soil_temp - soil_type: - name: soil_type - string_serialization: '{termLabel} [{termID}]' + class_uri: MIXS:0016022 + HostAssociated: + name: HostAssociated + description: host-associated extension + title: host-associated + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Extension + slots: + - samp_name + - project_name + - alt + - depth + - elev + - ances_data + - biol_stat + - genetic_mod + - host_common_name + - samp_capt_status + - samp_dis_stage + - host_taxid + - host_subject_id + - host_age + - host_life_stage + - host_sex + - host_disease_stat + - chem_administration + - host_body_habitat + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_length + - host_diet + - host_last_meal + - host_growth_cond + - host_substrate + - host_fam_rel + - host_subspecf_genlin + - host_genotype + - host_phenotype + - host_body_temp + - host_dry_mass + - blood_press_diast + - blood_press_syst + - host_color + - host_shape + - gravidity + - perturbation + - salinity + - oxy_stat_samp + - temp + - organism_count + - samp_vol_we_dna_ext + - samp_store_temp + - samp_store_dur + - samp_store_loc + - host_symbiont + - misc_param + slot_usage: + alt: + name: alt + recommended: true + chem_administration: + name: chem_administration + required: false + recommended: false + depth: + name: depth + examples: + - value: 10 meter + recommended: true + elev: + name: elev + recommended: true + gravidity: + name: gravidity + host_age: + name: host_age + examples: + - value: 10 days + required: false + recommended: false + host_body_habitat: + name: host_body_habitat + examples: + - value: nasopharynx + host_body_site: + name: host_body_site + examples: + - value: gill [UBERON:0002535] + host_body_temp: + name: host_body_temp + examples: + - value: 15 degree Celsius + host_color: + name: host_color + host_common_name: + name: host_common_name + examples: + - value: human + required: false + recommended: false + host_diet: + name: host_diet + examples: + - value: herbivore + host_disease_stat: + name: host_disease_stat + examples: + - value: rabies [DOID:11260] + required: false + recommended: false + host_fam_rel: + name: host_fam_rel + examples: + - value: offspring;Mussel25 + host_genotype: + name: host_genotype + examples: + - value: C57BL/6 + required: false + recommended: false + host_growth_cond: + name: host_growth_cond + host_height: + name: host_height + examples: + - value: 0.1 meter + required: false + recommended: false + host_last_meal: + name: host_last_meal + examples: + - value: corn feed;P2H + host_length: + name: host_length + required: false + recommended: false + host_life_stage: + name: host_life_stage + examples: + - value: adult + required: false + recommended: false + host_phenotype: + name: host_phenotype + examples: + - value: elongated [PATO:0001154] + required: false + recommended: false + host_shape: + name: host_shape + host_subject_id: + name: host_subject_id + examples: + - value: MPI123 + host_substrate: + name: host_substrate + host_symbiont: + name: host_symbiont + examples: + - value: flukeworms + host_taxid: + name: host_taxid + examples: + - value: '7955' + string_serialization: '{NCBI taxid}' required: false recommended: false - soil_type_meth: - name: soil_type_meth + host_tot_mass: + name: host_tot_mass + examples: + - value: 2500 gram required: false recommended: false - temp: - name: temp + organism_count: + name: organism_count + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR required: false recommended: false - tillage: - name: tillage + oxy_stat_samp: + name: oxy_stat_samp required: false recommended: false - tot_nitro_cont_meth: - name: tot_nitro_cont_meth + perturbation: + name: perturbation required: false recommended: false - tot_nitro_content: - name: tot_nitro_content + samp_store_dur: + name: samp_store_dur required: false recommended: false - tot_org_c_meth: - name: tot_org_c_meth + samp_store_loc: + name: samp_store_loc required: false recommended: false - tot_org_carb: - name: tot_org_carb + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext required: false recommended: false - turbidity: - name: turbidity - ventilation_type: - name: ventilation_type + temp: + name: temp required: false recommended: false - water_pH: - name: water_pH - description: pH measurement of the sample, or liquid portion of sample, or - aqueous phase of the fluid. - wind_direction: - name: wind_direction - examples: - - value: 0 degrees; Northwest - wind_speed: - name: wind_speed - examples: - - value: 1.6 kilometers per hour - class_uri: MIXS:0016020 - FoodFoodProductionFacility: - name: FoodFoodProductionFacility - description: food-food production facility extension - title: food-food production facility + class_uri: MIXS:0016002 + HumanAssociated: + name: HumanAssociated + description: human-associated extension + title: human-associated from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: - samp_name - project_name - - lat_lon - - geo_loc_name - - collection_date - - seq_meth - - samp_size - - samp_collect_device - - experimental_factor - - nucl_acid_ext + - host_subject_id + - host_age + - host_sex + - host_disease_stat + - ihmc_medication_code + - chem_administration + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_diet + - host_last_meal + - host_fam_rel + - host_genotype + - host_phenotype + - host_body_temp + - smoker + - host_hiv_stat + - drug_usage + - host_body_mass_index + - diet_last_six_month + - weight_loss_3_month + - ethnicity + - host_occupation + - pet_farm_animal + - travel_out_six_month + - twin_sibling + - medic_hist_perform + - study_complt_stat + - pulmonary_disord + - nose_throat_disord + - blood_blood_disord + - host_pulse + - gestation_state + - maternal_health_stat + - foetal_health_stat + - amniotic_fluid_color + - kidney_disord + - urogenit_tract_disor + - urine_collect_meth + - perturbation + - salinity + - oxy_stat_samp + - temp - organism_count + - samp_vol_we_dna_ext - samp_store_temp - samp_store_dur - - air_temp - - room_dim - - freq_clean - - samp_room_id - - samp_vol_we_dna_ext - - pool_dna_extracts + - host_symbiont - samp_store_loc - - surf_material - - indoor_surf - - avg_occup - - samp_floor - - genetic_mod - - coll_site_geo_feat - - samp_source_mat_cat - - samp_type - - samp_stor_media - - samp_stor_device - - food_product_type - - IFSAC_category - - food_product_qual - - food_contact_surf - - facility_type - - food_trav_mode - - food_trav_vehic - - samp_transport_dur - - samp_transport_temp - - samp_collect_method - - num_samp_collect - - lot_number - - hygienic_area - - env_monitoring_zone - - area_samp_size - - samp_surf_moisture - - samp_loc_condition - - biocide_used - - ster_meth_samp_room - - enrichment_protocol - - cult_target - - microb_cult_med - - timepoint - - bacterial_density - - cult_isol_date - - cult_result - - cult_result_org - - subspecf_gen_lin - - samp_pooling - - samp_purpose - - samp_rep_tech - - samp_rep_biol - - samp_transport_cont - - study_design - - nucl_acid_ext_kit - - library_prep_kit - - sequencing_kit - - sequencing_location - - study_inc_temp - - study_inc_dur - - study_timecourse - - study_tmnt - - food_source - - food_dis_point - - food_dis_point_city - - food_origin - - food_prod_synonym - - food_additive - - food_trace_list - - part_plant_animal - - food_ingredient - - spec_intended_cons - - HACCP_term - - dietary_claim_use - - food_allergen_label - - food_prod_char - - prod_label_claims - - food_name_status - - food_preserv_proc - - food_cooking_proc - - food_treat_proc - - food_contain_wrap - - food_pack_capacity - - food_pack_medium - - food_prior_contact - - food_prod - - food_quality_date - - repository_name - - intended_consumer - - food_pack_integrity - misc_param slot_usage: - air_temp: - name: air_temp - examples: - - value: 4 degree Celsius - required: false - recommended: false - avg_occup: - name: avg_occup - examples: - - value: '6' - enrichment_protocol: - name: enrichment_protocol - required: false - recommended: false - experimental_factor: - name: experimental_factor - required: false - recommended: false - food_contact_surf: - name: food_contact_surf - required: true - food_origin: - name: food_origin - required: false - recommended: false - food_pack_medium: - name: food_pack_medium - examples: - - value: vacuum-packed [FOODON:03480027] - food_prod: - name: food_prod - required: false - recommended: false - food_product_qual: - name: food_product_qual - required: true - food_product_type: - name: food_product_type - examples: - - value: shrimp (peeled, deep-frozen) [FOODON:03317171] - required: true - food_source: - name: food_source - examples: - - value: giant tiger prawn [FOODON:03412612] - required: false - recommended: false - freq_clean: - name: freq_clean - string_serialization: '{text}' - indoor_surf: - name: indoor_surf + chem_administration: + name: chem_administration required: false recommended: false - intended_consumer: - name: intended_consumer + host_age: + name: host_age + examples: + - value: 30 years required: false recommended: false - library_prep_kit: - name: library_prep_kit + host_body_site: + name: host_body_site examples: - - value: Illumina DNA Prep - nucl_acid_ext: - name: nucl_acid_ext + - value: Lung parenchyma [fma27360] + host_body_temp: + name: host_body_temp + examples: + - value: 36.5 degree Celsius + host_diet: + name: host_diet + examples: + - value: high-fat + host_disease_stat: + name: host_disease_stat + examples: + - value: measles [DOID:8622] required: false recommended: false - organism_count: - name: organism_count + host_fam_rel: + name: host_fam_rel examples: - - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR + - value: mother;ID298 + host_genotype: + name: host_genotype + examples: + - value: ST1 required: false recommended: false - pool_dna_extracts: - name: pool_dna_extracts - string_serialization: '{boolean},{integer}' + host_height: + name: host_height + examples: + - value: 1.75 meter required: false recommended: false - samp_collect_device: - name: samp_collect_device + host_last_meal: + name: host_last_meal examples: - - value: biopsy, niskin bottle, push core + - value: french fries;P5H30M + host_phenotype: + name: host_phenotype + examples: + - value: Tinnitus [HP:0000360] required: false recommended: false - samp_collect_method: - name: samp_collect_method + host_subject_id: + name: host_subject_id examples: - - value: environmental swab sampling + - value: MPI123 + host_symbiont: + name: host_symbiont + examples: + - value: flukeworms + host_tot_mass: + name: host_tot_mass + examples: + - value: 65 kilogram required: false recommended: false - samp_pooling: - name: samp_pooling + organism_count: + name: organism_count + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR required: false recommended: false - samp_purpose: - name: samp_purpose + oxy_stat_samp: + name: oxy_stat_samp required: false recommended: false - samp_size: - name: samp_size + perturbation: + name: perturbation required: false recommended: false - samp_source_mat_cat: - name: samp_source_mat_cat - required: true - samp_stor_device: - name: samp_stor_device - required: true - samp_stor_media: - name: samp_stor_media - required: true samp_store_dur: name: samp_store_dur required: false @@ -21826,230 +25249,279 @@ classes: name: samp_vol_we_dna_ext required: false recommended: false - subspecf_gen_lin: - name: subspecf_gen_lin - surf_material: - name: surf_material + temp: + name: temp required: false recommended: false - class_uri: MIXS:0016021 - FoodHumanFoods: - name: FoodHumanFoods - description: food-human foods extension - title: food-human foods + class_uri: MIXS:0016003 + HumanGut: + name: HumanGut + description: human-gut extension + title: human-gut from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: - samp_name - project_name - - lat_lon - - geo_loc_name - - collection_date - - seq_meth - - samp_size - - samp_collect_device - - experimental_factor - - nucl_acid_ext + - gastrointest_disord + - liver_disord + - special_diet + - host_subject_id + - host_age + - host_sex + - host_disease_stat + - ihmc_medication_code + - chem_administration + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_diet + - host_last_meal + - host_fam_rel + - host_genotype + - host_phenotype + - host_body_temp + - host_body_mass_index + - ethnicity + - host_occupation + - medic_hist_perform + - host_pulse + - perturbation + - salinity + - oxy_stat_samp + - temp - organism_count - - spikein_count - samp_store_temp - - samp_store_dur - samp_vol_we_dna_ext - - pool_dna_extracts - - temp + - samp_store_dur + - host_symbiont - samp_store_loc - - genetic_mod - - perturbation - - coll_site_geo_feat - - food_product_type - - IFSAC_category - - ferm_chem_add - - ferm_chem_add_perc - - ferm_headspace_oxy - - ferm_medium - - ferm_pH - - ferm_rel_humidity - - ferm_temp - - ferm_time - - ferm_vessel - - bacterial_density - - cons_food_stor_dur - - cons_food_stor_temp - - cons_purch_date - - cons_qty_purchased - - cult_isol_date - - cult_result - - cult_result_org - - cult_target - - dietary_claim_use - - enrichment_protocol - - food_additive - - food_allergen_label - - food_contact_surf - - food_contain_wrap - - food_cooking_proc - - food_dis_point - - food_ingredient - - food_name_status - - food_origin - - food_pack_capacity - - food_pack_integrity - - food_pack_medium - - food_preserv_proc - - food_prior_contact - - food_prod - - food_prod_synonym - - food_product_qual - - food_quality_date - - food_source - - food_trace_list - - food_trav_mode - - food_trav_vehic - - food_treat_proc - - HACCP_term - - intended_consumer - - library_prep_kit - - lot_number - - microb_cult_med - - microb_start - - microb_start_count - - microb_start_inoc - - microb_start_prep - - microb_start_source - - microb_start_taxID - - nucl_acid_ext_kit - - num_samp_collect - - part_plant_animal - - repository_name - - samp_collect_method - - samp_pooling - - samp_rep_biol - - samp_rep_tech - - samp_source_mat_cat - - samp_stor_device - - samp_stor_media - - samp_transport_cont - - samp_transport_dur - - samp_transport_temp - - samp_purpose - - sequencing_kit - - sequencing_location - - serovar_or_serotype - - spikein_AMR - - spikein_antibiotic - - spikein_growth_med - - spikein_metal - - spikein_org - - spikein_serovar - - spikein_strain - - study_design - - study_inc_dur - - study_inc_temp - - study_timecourse - - study_tmnt - - timepoint - misc_param slot_usage: - enrichment_protocol: - name: enrichment_protocol - required: false - recommended: false - experimental_factor: - name: experimental_factor - required: false - recommended: false - food_contact_surf: - name: food_contact_surf + chem_administration: + name: chem_administration required: false recommended: false - food_origin: - name: food_origin + host_age: + name: host_age + examples: + - value: 30 years required: false recommended: false - food_pack_medium: - name: food_pack_medium + host_body_site: + name: host_body_site examples: - - value: vacuum-packed[FOODON:03480027] - food_prod: - name: food_prod + - value: Wall of gut [fma45653] + host_body_temp: + name: host_body_temp + examples: + - value: 36.5 degree Celsius + host_diet: + name: host_diet + examples: + - value: high-fat + host_disease_stat: + name: host_disease_stat + examples: + - value: measles [DOID:8622] required: false recommended: false - food_product_qual: - name: food_product_qual + host_fam_rel: + name: host_fam_rel + examples: + - value: mother;ID298 + host_genotype: + name: host_genotype + examples: + - value: ST1 required: false recommended: false - food_product_type: - name: food_product_type - examples: - - value: shrimp (peeled, deep-frozen) [FOODON:03317171] - required: true - food_source: - name: food_source + host_height: + name: host_height examples: - - value: giant tiger prawn [FOODON:03412612] + - value: 1.75 meter required: false recommended: false - intended_consumer: - name: intended_consumer + host_last_meal: + name: host_last_meal + examples: + - value: french fries;P5H30M + host_phenotype: + name: host_phenotype + examples: + - value: Tinnitus [HP:0000360] required: false recommended: false - library_prep_kit: - name: library_prep_kit + host_subject_id: + name: host_subject_id examples: - - value: Illumina DNA Prep - nucl_acid_ext: - name: nucl_acid_ext + - value: MPI123 + host_symbiont: + name: host_symbiont + examples: + - value: flukeworms + host_tot_mass: + name: host_tot_mass + examples: + - value: 65 kilogram required: false recommended: false organism_count: name: organism_count examples: - - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + required: false + recommended: false + oxy_stat_samp: + name: oxy_stat_samp required: false recommended: false perturbation: name: perturbation required: false recommended: false - pool_dna_extracts: - name: pool_dna_extracts - string_serialization: '{boolean},{integer}' + samp_store_dur: + name: samp_store_dur required: false recommended: false - samp_collect_device: - name: samp_collect_device + samp_store_loc: + name: samp_store_loc + required: false + recommended: false + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + required: false + recommended: false + temp: + name: temp + required: false + recommended: false + class_uri: MIXS:0016004 + HumanOral: + name: HumanOral + description: human-oral extension + title: human-oral + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Extension + slots: + - samp_name + - project_name + - nose_mouth_teeth_throat_disord + - time_last_toothbrush + - host_subject_id + - host_age + - host_sex + - host_disease_stat + - ihmc_medication_code + - chem_administration + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_diet + - host_last_meal + - host_fam_rel + - host_genotype + - host_phenotype + - host_body_temp + - host_body_mass_index + - ethnicity + - host_occupation + - medic_hist_perform + - host_pulse + - perturbation + - salinity + - oxy_stat_samp + - temp + - organism_count + - samp_vol_we_dna_ext + - samp_store_temp + - samp_store_dur + - host_symbiont + - samp_store_loc + - misc_param + slot_usage: + chem_administration: + name: chem_administration + required: false + recommended: false + host_age: + name: host_age examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + - value: 30 years required: false recommended: false - samp_collect_method: - name: samp_collect_method + host_body_site: + name: host_body_site examples: - - value: environmental swab sampling + - value: Epithelium of tongue [fma284658] + host_body_temp: + name: host_body_temp + examples: + - value: 36.5 degree Celsius + host_diet: + name: host_diet + examples: + - value: high-fat + host_disease_stat: + name: host_disease_stat + examples: + - value: measles [DOID:8622] required: false recommended: false - samp_pooling: - name: samp_pooling + host_fam_rel: + name: host_fam_rel + examples: + - value: mother;ID298 + host_genotype: + name: host_genotype + examples: + - value: ST1 required: false recommended: false - samp_purpose: - name: samp_purpose + host_height: + name: host_height + examples: + - value: 1.75 meter required: false recommended: false - samp_size: - name: samp_size + host_last_meal: + name: host_last_meal + examples: + - value: french fries;P5H30M + host_phenotype: + name: host_phenotype + examples: + - value: Tinnitus [HP:0000360] required: false recommended: false - samp_source_mat_cat: - name: samp_source_mat_cat + host_subject_id: + name: host_subject_id + examples: + - value: MPI123 + host_symbiont: + name: host_symbiont + examples: + - value: flukeworms + host_tot_mass: + name: host_tot_mass + examples: + - value: 65 kilogram required: false recommended: false - samp_stor_device: - name: samp_stor_device + organism_count: + name: organism_count + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR required: false recommended: false - samp_stor_media: - name: samp_stor_media + oxy_stat_samp: + name: oxy_stat_samp + required: false + recommended: false + perturbation: + name: perturbation required: false recommended: false samp_store_dur: @@ -22068,53 +25540,40 @@ classes: name: temp required: false recommended: false - class_uri: MIXS:0016022 - HostAssociated: - name: HostAssociated - description: host-associated extension - title: host-associated + class_uri: MIXS:0016005 + HumanSkin: + name: HumanSkin + description: human-skin extension + title: human-skin from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: - samp_name - project_name - - alt - - depth - - elev - - ances_data - - biol_stat - - genetic_mod - - host_common_name - - samp_capt_status - - samp_dis_stage - - host_taxid + - dermatology_disord + - time_since_last_wash + - dominant_hand - host_subject_id - host_age - - host_life_stage - host_sex - host_disease_stat + - ihmc_medication_code - chem_administration - - host_body_habitat - host_body_site - host_body_product - host_tot_mass - host_height - - host_length - host_diet - host_last_meal - - host_growth_cond - - host_substrate - host_fam_rel - - host_subspecf_genlin - host_genotype - host_phenotype - host_body_temp - - host_dry_mass - - blood_press_diast - - blood_press_syst - - host_color - - host_shape - - gravidity + - host_body_mass_index + - ethnicity + - host_occupation + - medic_hist_perform + - host_pulse - perturbation - salinity - oxy_stat_samp @@ -22127,120 +25586,72 @@ classes: - host_symbiont - misc_param slot_usage: - alt: - name: alt - recommended: true chem_administration: name: chem_administration required: false recommended: false - depth: - name: depth - examples: - - value: 10 meter - recommended: true - elev: - name: elev - recommended: true - gravidity: - name: gravidity host_age: name: host_age examples: - - value: 10 days + - value: 30 years required: false recommended: false - host_body_habitat: - name: host_body_habitat - examples: - - value: nasopharynx host_body_site: name: host_body_site examples: - - value: gill [UBERON:0002535] + - value: Skin of palm of left hand [fma38303] host_body_temp: name: host_body_temp examples: - - value: 15 degree Celsius - host_color: - name: host_color - host_common_name: - name: host_common_name - examples: - - value: human - required: false - recommended: false + - value: 36.5 degree Celsius host_diet: name: host_diet examples: - - value: herbivore + - value: high-fat host_disease_stat: name: host_disease_stat examples: - - value: rabies [DOID:11260] + - value: measles [DOID:8622] required: false recommended: false host_fam_rel: name: host_fam_rel examples: - - value: offspring;Mussel25 + - value: mother;ID298 host_genotype: name: host_genotype examples: - - value: C57BL/6 + - value: ST1 required: false recommended: false - host_growth_cond: - name: host_growth_cond host_height: name: host_height examples: - - value: 0.1 meter + - value: 1.75 meter required: false recommended: false host_last_meal: name: host_last_meal examples: - - value: corn feed;P2H - host_length: - name: host_length - required: false - recommended: false - host_life_stage: - name: host_life_stage - examples: - - value: adult - required: false - recommended: false + - value: french fries;P5H30M host_phenotype: name: host_phenotype examples: - - value: elongated [PATO:0001154] + - value: Tinnitus [HP:0000360] required: false recommended: false - host_shape: - name: host_shape host_subject_id: name: host_subject_id examples: - value: MPI123 - host_substrate: - name: host_substrate host_symbiont: name: host_symbiont examples: - value: flukeworms - host_taxid: - name: host_taxid - examples: - - value: '7955' - string_serialization: '{NCBI taxid}' - required: false - recommended: false host_tot_mass: name: host_tot_mass examples: - - value: 2500 gram + - value: 65 kilogram required: false recommended: false organism_count: @@ -22273,16 +25684,26 @@ classes: name: temp required: false recommended: false - class_uri: MIXS:0016002 - HumanAssociated: - name: HumanAssociated - description: human-associated extension - title: human-associated + class_uri: MIXS:0016006 + HumanVaginal: + name: HumanVaginal + description: human-vaginal extension + title: human-vaginal from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: - samp_name - project_name + - menarche + - sexual_act + - pregnancy + - douche + - birth_control + - menopause + - hrt + - hysterectomy + - gynecologic_disord + - urogenit_disord - host_subject_id - host_age - host_sex @@ -22299,30 +25720,11 @@ classes: - host_genotype - host_phenotype - host_body_temp - - smoker - - host_hiv_stat - - drug_usage - host_body_mass_index - - diet_last_six_month - - weight_loss_3_month - ethnicity - host_occupation - - pet_farm_animal - - travel_out_six_month - - twin_sibling - medic_hist_perform - - study_complt_stat - - pulmonary_disord - - nose_throat_disord - - blood_blood_disord - host_pulse - - gestation_state - - maternal_health_stat - - foetal_health_stat - - amniotic_fluid_color - - kidney_disord - - urogenit_tract_disor - - urine_collect_meth - perturbation - salinity - oxy_stat_samp @@ -22330,9 +25732,9 @@ classes: - organism_count - samp_vol_we_dna_ext - samp_store_temp + - samp_store_loc - samp_store_dur - host_symbiont - - samp_store_loc - misc_param slot_usage: chem_administration: @@ -22348,7 +25750,7 @@ classes: host_body_site: name: host_body_site examples: - - value: Lung parenchyma [fma27360] + - value: Ectocervix [fma86484] host_body_temp: name: host_body_temp examples: @@ -22427,140 +25829,290 @@ classes: recommended: false samp_vol_we_dna_ext: name: samp_vol_we_dna_ext - required: false - recommended: false + required: false + recommended: false + temp: + name: temp + required: false + recommended: false + class_uri: MIXS:0016007 + HydrocarbonResourcesCores: + name: HydrocarbonResourcesCores + description: hydrocarbon resources-cores extension + title: hydrocarbon resources-cores + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Extension + slots: + - samp_name + - project_name + - hcr + - hc_produced + - basin + - field + - reservoir + - hcr_temp + - tvdss_of_hcr_temp + - hcr_pressure + - tvdss_of_hcr_press + - permeability + - porosity + - lithology + - depos_env + - hcr_geol_age + - owc_tvdss + - hcr_fw_salinity + - sulfate_fw + - vfa_fw + - sr_kerog_type + - sr_lithology + - sr_dep_env + - sr_geol_age + - samp_well_name + - win + - samp_type + - samp_subtype + - temp + - pressure + - samp_tvdss + - samp_md + - elev + - oxy_stat_samp + - samp_transport_cond + - samp_store_temp + - samp_store_dur + - samp_store_loc + - samp_vol_we_dna_ext + - organism_count + - org_count_qpcr_info + - ph + - salinity + - alkalinity + - alkalinity_method + - sulfate + - sulfide + - tot_sulfur + - nitrate + - nitrite + - ammonium + - tot_nitro + - diss_iron + - sodium + - chloride + - potassium + - magnesium + - calcium + - tot_iron + - diss_org_carb + - diss_inorg_carb + - diss_inorg_phosp + - tot_phosp + - suspend_solids + - density + - diss_carb_dioxide + - diss_oxygen_fluid + - vfa + - benzene + - toluene + - ethylbenzene + - xylene + - api + - tan + - viscosity + - pour_point + - saturates_pc + - aromatics_pc + - resins_pc + - asphaltenes_pc + - misc_param + - additional_info + slot_usage: + ammonium: + name: ammonium + recommended: true + depos_env: + name: depos_env + examples: + - value: Continental - Alluvial + diss_inorg_phosp: + name: diss_inorg_phosp + recommended: true + elev: + name: elev + required: false + recommended: false + hcr_temp: + name: hcr_temp + required: true + nitrate: + name: nitrate + recommended: true + nitrite: + name: nitrite + recommended: true + organism_count: + name: organism_count + examples: + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR + recommended: true + oxy_stat_samp: + name: oxy_stat_samp + required: false + recommended: false + ph: + name: ph + recommended: true + samp_store_dur: + name: samp_store_dur + required: false + recommended: false + samp_store_loc: + name: samp_store_loc + required: false + recommended: false + samp_vol_we_dna_ext: + name: samp_vol_we_dna_ext + recommended: true + sulfate: + name: sulfate + recommended: true + sulfate_fw: + name: sulfate_fw + required: true + sulfide: + name: sulfide + recommended: true temp: name: temp - required: false - recommended: false - class_uri: MIXS:0016003 - HumanGut: - name: HumanGut - description: human-gut extension - title: human-gut + required: true + vfa_fw: + name: vfa_fw + required: true + class_uri: MIXS:0016015 + HydrocarbonResourcesFluidsSwabs: + name: HydrocarbonResourcesFluidsSwabs + description: hydrocarbon resources-fluids/swabs extension + title: hydrocarbon resources-fluids/swabs from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: - samp_name - project_name - - gastrointest_disord - - liver_disord - - special_diet - - host_subject_id - - host_age - - host_sex - - host_disease_stat - - ihmc_medication_code - - chem_administration - - host_body_site - - host_body_product - - host_tot_mass - - host_height - - host_diet - - host_last_meal - - host_fam_rel - - host_genotype - - host_phenotype - - host_body_temp - - host_body_mass_index - - ethnicity - - host_occupation - - medic_hist_perform - - host_pulse - - perturbation - - salinity - - oxy_stat_samp + - hcr + - hc_produced + - basin + - field + - reservoir + - hcr_temp + - tvdss_of_hcr_temp + - hcr_pressure + - tvdss_of_hcr_press + - lithology + - depos_env + - hcr_geol_age + - hcr_fw_salinity + - sulfate_fw + - vfa_fw + - prod_start_date + - prod_rate + - water_prod_rate + - water_cut + - iwf + - add_recov_method + - iw_bt_date_well + - biocide + - biocide_admin_method + - chem_treatment + - chem_treat_method + - samp_loc_corr_rate + - samp_well_name + - win + - samp_type + - samp_subtype + - samp_collect_point - temp - - organism_count + - pressure + - oxy_stat_samp + - samp_preserv + - samp_transport_cond - samp_store_temp - - samp_vol_we_dna_ext - samp_store_dur - - host_symbiont - samp_store_loc + - samp_vol_we_dna_ext + - organism_count + - org_count_qpcr_info + - ph + - salinity + - alkalinity + - alkalinity_method + - sulfate + - sulfide + - tot_sulfur + - nitrate + - nitrite + - ammonium + - tot_nitro + - diss_iron + - sodium + - chloride + - potassium + - magnesium + - calcium + - tot_iron + - diss_org_carb + - diss_inorg_carb + - diss_inorg_phosp + - tot_phosp + - suspend_solids + - density + - diss_carb_dioxide + - diss_oxygen_fluid + - vfa + - benzene + - toluene + - ethylbenzene + - xylene + - api + - tan + - viscosity + - pour_point + - saturates_pc + - aromatics_pc + - resins_pc + - asphaltenes_pc - misc_param + - additional_info slot_usage: - chem_administration: - name: chem_administration - required: false - recommended: false - host_age: - name: host_age - examples: - - value: 30 years - required: false - recommended: false - host_body_site: - name: host_body_site - examples: - - value: Wall of gut [fma45653] - host_body_temp: - name: host_body_temp - examples: - - value: 36.5 degree Celsius - host_diet: - name: host_diet - examples: - - value: high-fat - host_disease_stat: - name: host_disease_stat - examples: - - value: measles [DOID:8622] - required: false - recommended: false - host_fam_rel: - name: host_fam_rel - examples: - - value: mother;ID298 - host_genotype: - name: host_genotype - examples: - - value: ST1 - required: false - recommended: false - host_height: - name: host_height - examples: - - value: 1.75 meter - required: false - recommended: false - host_last_meal: - name: host_last_meal - examples: - - value: french fries;P5H30M - host_phenotype: - name: host_phenotype - examples: - - value: Tinnitus [HP:0000360] - required: false - recommended: false - host_subject_id: - name: host_subject_id - examples: - - value: MPI123 - host_symbiont: - name: host_symbiont - examples: - - value: flukeworms - host_tot_mass: - name: host_tot_mass + ammonium: + name: ammonium + recommended: true + depos_env: + name: depos_env examples: - - value: 65 kilogram - required: false - recommended: false + - value: Marine - Reef + diss_inorg_phosp: + name: diss_inorg_phosp + recommended: true + hcr_temp: + name: hcr_temp + recommended: true + nitrate: + name: nitrate + required: true + nitrite: + name: nitrite + recommended: true organism_count: name: organism_count examples: - value: total prokaryotes;3.5e7 cells per milliliter;qPCR - required: false - recommended: false + recommended: true oxy_stat_samp: name: oxy_stat_samp required: false recommended: false - perturbation: - name: perturbation - required: false - recommended: false + ph: + name: ph + recommended: true samp_store_dur: name: samp_store_dur required: false @@ -22571,125 +26123,135 @@ classes: recommended: false samp_vol_we_dna_ext: name: samp_vol_we_dna_ext - required: false - recommended: false + recommended: true + sulfate: + name: sulfate + required: true + sulfate_fw: + name: sulfate_fw + recommended: true + sulfide: + name: sulfide + required: true temp: name: temp - required: false - recommended: false - class_uri: MIXS:0016004 - HumanOral: - name: HumanOral - description: human-oral extension - title: human-oral + required: true + vfa_fw: + name: vfa_fw + recommended: true + class_uri: MIXS:0016016 + MicrobialMatBiofilm: + name: MicrobialMatBiofilm + description: microbial mat/biofilm extension + title: microbial mat/biofilm from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: - samp_name - project_name - - nose_mouth_teeth_throat_disord - - time_last_toothbrush - - host_subject_id - - host_age - - host_sex - - host_disease_stat - - ihmc_medication_code + - depth + - elev + - alkalinity + - alkyl_diethers + - aminopept_act + - ammonium + - bacteria_carb_prod + - biomass + - bishomohopanol + - bromide + - calcium + - carb_nitro_ratio - chem_administration - - host_body_site - - host_body_product - - host_tot_mass - - host_height - - host_diet - - host_last_meal - - host_fam_rel - - host_genotype - - host_phenotype - - host_body_temp - - host_body_mass_index - - ethnicity - - host_occupation - - medic_hist_perform - - host_pulse + - chloride + - chlorophyll + - diether_lipids + - diss_carb_dioxide + - diss_hydrogen + - diss_inorg_carb + - diss_org_carb + - diss_org_nitro + - diss_oxygen + - glucosidase_act + - magnesium + - mean_frict_vel + - mean_peak_frict_vel + - methane + - misc_param + - n_alkanes + - nitrate + - nitrite + - nitro + - org_carb + - org_matter + - org_nitro + - organism_count + - oxy_stat_samp + - ph + - part_org_carb - perturbation + - petroleum_hydrocarb + - phaeopigments + - phosphate + - phosplipid_fatt_acid + - potassium + - pressure + - redox_potential - salinity - - oxy_stat_samp - - temp - - organism_count - - samp_vol_we_dna_ext - - samp_store_temp - samp_store_dur - - host_symbiont - samp_store_loc - - misc_param + - samp_store_temp + - samp_vol_we_dna_ext + - silicate + - sodium + - sulfate + - sulfide + - temp + - tot_carb + - tot_nitro_content + - tot_org_carb + - turbidity + - water_content slot_usage: - chem_administration: - name: chem_administration - required: false - recommended: false - host_age: - name: host_age - examples: - - value: 30 years - required: false - recommended: false - host_body_site: - name: host_body_site - examples: - - value: Epithelium of tongue [fma284658] - host_body_temp: - name: host_body_temp - examples: - - value: 36.5 degree Celsius - host_diet: - name: host_diet - examples: - - value: high-fat - host_disease_stat: - name: host_disease_stat - examples: - - value: measles [DOID:8622] - required: false - recommended: false - host_fam_rel: - name: host_fam_rel - examples: - - value: mother;ID298 - host_genotype: - name: host_genotype - examples: - - value: ST1 + alkyl_diethers: + name: alkyl_diethers + ammonium: + name: ammonium required: false recommended: false - host_height: - name: host_height - examples: - - value: 1.75 meter + bacteria_carb_prod: + name: bacteria_carb_prod + chem_administration: + name: chem_administration required: false recommended: false - host_last_meal: - name: host_last_meal + depth: + name: depth examples: - - value: french fries;P5H30M - host_phenotype: - name: host_phenotype + - value: 10 meter + recommended: true + diss_org_nitro: + name: diss_org_nitro + elev: + name: elev + recommended: true + methane: + name: methane examples: - - value: Tinnitus [HP:0000360] + - value: 0.15 micromole per liter + n_alkanes: + name: n_alkanes + nitrate: + name: nitrate required: false recommended: false - host_subject_id: - name: host_subject_id - examples: - - value: MPI123 - host_symbiont: - name: host_symbiont - examples: - - value: flukeworms - host_tot_mass: - name: host_tot_mass - examples: - - value: 65 kilogram + nitrite: + name: nitrite required: false recommended: false + org_carb: + name: org_carb + org_nitro: + name: org_nitro organism_count: name: organism_count examples: @@ -22700,10 +26262,18 @@ classes: name: oxy_stat_samp required: false recommended: false + part_org_carb: + name: part_org_carb perturbation: name: perturbation required: false recommended: false + ph: + name: ph + required: false + recommended: false + phosplipid_fatt_acid: + name: phosplipid_fatt_acid samp_store_dur: name: samp_store_dur required: false @@ -22716,124 +26286,123 @@ classes: name: samp_vol_we_dna_ext required: false recommended: false + sulfate: + name: sulfate + required: false + recommended: false + sulfide: + name: sulfide + required: false + recommended: false temp: name: temp required: false recommended: false - class_uri: MIXS:0016005 - HumanSkin: - name: HumanSkin - description: human-skin extension - title: human-skin + tot_carb: + name: tot_carb + required: false + recommended: false + tot_nitro_content: + name: tot_nitro_content + required: false + recommended: false + tot_org_carb: + name: tot_org_carb + required: false + recommended: false + turbidity: + name: turbidity + water_content: + name: water_content + string_serialization: '{float} {unit}' + class_uri: MIXS:0016008 + MiscellaneousNaturalOrArtificialEnvironment: + name: MiscellaneousNaturalOrArtificialEnvironment + description: miscellaneous natural or artificial environment extension + title: miscellaneous natural or artificial environment from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: - samp_name - project_name - - dermatology_disord - - time_since_last_wash - - dominant_hand - - host_subject_id - - host_age - - host_sex - - host_disease_stat - - ihmc_medication_code + - alt + - depth + - elev + - alkalinity + - ammonium + - biomass + - bromide + - calcium - chem_administration - - host_body_site - - host_body_product - - host_tot_mass - - host_height - - host_diet - - host_last_meal - - host_fam_rel - - host_genotype - - host_phenotype - - host_body_temp - - host_body_mass_index - - ethnicity - - host_occupation - - medic_hist_perform - - host_pulse + - chloride + - chlorophyll + - density + - diether_lipids + - diss_carb_dioxide + - diss_hydrogen + - diss_inorg_carb + - diss_org_nitro + - diss_oxygen + - misc_param + - nitrate + - nitrite + - nitro + - org_carb + - org_matter + - org_nitro + - organism_count + - oxy_stat_samp + - ph - perturbation + - phosphate + - phosplipid_fatt_acid + - potassium + - pressure - salinity - - oxy_stat_samp - - temp - - organism_count - - samp_vol_we_dna_ext - - samp_store_temp - samp_store_dur - samp_store_loc - - host_symbiont - - misc_param + - samp_store_temp + - samp_vol_we_dna_ext + - silicate + - sodium + - sulfate + - sulfide + - temp + - water_current slot_usage: - chem_administration: - name: chem_administration - required: false - recommended: false - host_age: - name: host_age - examples: - - value: 30 years - required: false - recommended: false - host_body_site: - name: host_body_site - examples: - - value: Skin of palm of left hand [fma38303] - host_body_temp: - name: host_body_temp - examples: - - value: 36.5 degree Celsius - host_diet: - name: host_diet - examples: - - value: high-fat - host_disease_stat: - name: host_disease_stat - examples: - - value: measles [DOID:8622] - required: false - recommended: false - host_fam_rel: - name: host_fam_rel - examples: - - value: mother;ID298 - host_genotype: - name: host_genotype - examples: - - value: ST1 + alt: + name: alt + recommended: true + ammonium: + name: ammonium required: false recommended: false - host_height: - name: host_height - examples: - - value: 1.75 meter + chem_administration: + name: chem_administration required: false recommended: false - host_last_meal: - name: host_last_meal - examples: - - value: french fries;P5H30M - host_phenotype: - name: host_phenotype + depth: + name: depth examples: - - value: Tinnitus [HP:0000360] + - value: 10 meter + recommended: true + diss_org_nitro: + name: diss_org_nitro + elev: + name: elev + recommended: true + nitrate: + name: nitrate required: false recommended: false - host_subject_id: - name: host_subject_id - examples: - - value: MPI123 - host_symbiont: - name: host_symbiont - examples: - - value: flukeworms - host_tot_mass: - name: host_tot_mass - examples: - - value: 65 kilogram + nitrite: + name: nitrite required: false recommended: false + org_carb: + name: org_carb + org_nitro: + name: org_nitro organism_count: name: organism_count examples: @@ -22848,6 +26417,12 @@ classes: name: perturbation required: false recommended: false + ph: + name: ph + required: false + recommended: false + phosplipid_fatt_acid: + name: phosplipid_fatt_acid samp_store_dur: name: samp_store_dur required: false @@ -22860,129 +26435,204 @@ classes: name: samp_vol_we_dna_ext required: false recommended: false + sulfate: + name: sulfate + required: false + recommended: false + sulfide: + name: sulfide + required: false + recommended: false temp: name: temp required: false recommended: false - class_uri: MIXS:0016006 - HumanVaginal: - name: HumanVaginal - description: human-vaginal extension - title: human-vaginal + class_uri: MIXS:0016009 + PlantAssociated: + name: PlantAssociated + description: plant-associated extension + title: plant-associated from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: - samp_name - project_name - - menarche - - sexual_act - - pregnancy - - douche - - birth_control - - menopause - - hrt - - hysterectomy - - gynecologic_disord - - urogenit_disord - - host_subject_id + - depth + - elev + - air_temp_regm + - ances_data + - antibiotic_regm + - biol_stat + - biotic_regm + - chem_administration + - chem_mutagen + - climate_environment + - cult_root_med + - fertilizer_regm + - fungicide_regm + - gaseous_environment + - genetic_mod + - gravity + - growth_facil + - growth_habit + - growth_hormone_regm + - herbicide_regm - host_age - - host_sex + - host_common_name - host_disease_stat - - ihmc_medication_code - - chem_administration - - host_body_site - - host_body_product - - host_tot_mass - - host_height - - host_diet - - host_last_meal - - host_fam_rel + - host_dry_mass - host_genotype + - host_height + - host_subspecf_genlin + - host_length + - host_life_stage - host_phenotype - - host_body_temp - - host_body_mass_index - - ethnicity - - host_occupation - - medic_hist_perform - - host_pulse + - host_taxid + - host_tot_mass + - host_wet_mass + - humidity_regm + - light_regm + - mechanical_damage + - mineral_nutr_regm + - misc_param + - non_min_nutr_regm + - organism_count + - oxy_stat_samp + - ph_regm - perturbation + - pesticide_regm + - plant_growth_med + - plant_product + - plant_sex + - plant_struc + - radiation_regm + - rainfall_regm + - root_cond + - root_med_carbon + - root_med_macronutr + - root_med_micronutr + - root_med_suppl + - root_med_ph + - root_med_regl + - root_med_solid + - salt_regm + - samp_capt_status + - samp_dis_stage - salinity - - oxy_stat_samp - - temp - - organism_count - - samp_vol_we_dna_ext - - samp_store_temp - - samp_store_loc - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - season_environment + - standing_water_regm + - temp + - tiss_cult_growth_med + - water_temp_regm + - watering_regm - host_symbiont - - misc_param slot_usage: + biotic_regm: + name: biotic_regm + required: false + recommended: false chem_administration: name: chem_administration required: false recommended: false + climate_environment: + name: climate_environment + string_serialization: '{text};{Rn/start_time/end_time/duration}' + required: false + recommended: false + depth: + name: depth + examples: + - value: 10 meter + recommended: true + elev: + name: elev + recommended: true + fungicide_regm: + name: fungicide_regm + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + required: false + recommended: false + gaseous_environment: + name: gaseous_environment + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + required: false + recommended: false + herbicide_regm: + name: herbicide_regm + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + required: false + recommended: false host_age: name: host_age examples: - - value: 30 years + - value: 10 days required: false recommended: false - host_body_site: - name: host_body_site - examples: - - value: Ectocervix [fma86484] - host_body_temp: - name: host_body_temp - examples: - - value: 36.5 degree Celsius - host_diet: - name: host_diet + host_common_name: + name: host_common_name examples: - - value: high-fat + - value: rice + required: false + recommended: false host_disease_stat: name: host_disease_stat examples: - - value: measles [DOID:8622] + - value: downy mildew required: false recommended: false - host_fam_rel: - name: host_fam_rel - examples: - - value: mother;ID298 host_genotype: name: host_genotype examples: - - value: ST1 + - value: Ts required: false recommended: false host_height: name: host_height examples: - - value: 1.75 meter + - value: 1 meter required: false recommended: false - host_last_meal: - name: host_last_meal + host_length: + name: host_length + required: false + recommended: false + host_life_stage: + name: host_life_stage examples: - - value: french fries;P5H30M + - value: adult + required: false + recommended: false host_phenotype: name: host_phenotype examples: - - value: Tinnitus [HP:0000360] + - value: seed pod; green [PATO:0000320] required: false recommended: false - host_subject_id: - name: host_subject_id - examples: - - value: MPI123 host_symbiont: name: host_symbiont examples: - value: flukeworms + host_taxid: + name: host_taxid + examples: + - value: '4530' + string_serialization: '{NCBI taxid}' + required: false + recommended: false host_tot_mass: name: host_tot_mass examples: - - value: 65 kilogram + - value: 2500 gram + required: false + recommended: false + non_min_nutr_regm: + name: non_min_nutr_regm + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' required: false recommended: false organism_count: @@ -22999,6 +26649,33 @@ classes: name: perturbation required: false recommended: false + pesticide_regm: + name: pesticide_regm + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + required: false + recommended: false + ph_regm: + name: ph_regm + string_serialization: '{float};{Rn/start_time/end_time/duration}' + required: false + recommended: false + plant_growth_med: + name: plant_growth_med + examples: + - value: hydroponic plant culture media [EO:0007067] + plant_product: + name: plant_product + required: false + recommended: false + plant_struc: + name: plant_struc + required: false + recommended: false + salt_regm: + name: salt_regm + string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + required: false + recommended: false samp_store_dur: name: samp_store_dur required: false @@ -23011,136 +26688,171 @@ classes: name: samp_vol_we_dna_ext required: false recommended: false + season_environment: + name: season_environment + string_serialization: '{text};{Rn/start_time/end_time/duration}' + required: false + recommended: false + standing_water_regm: + name: standing_water_regm + string_serialization: '{text};{Rn/start_time/end_time/duration}' + required: false + recommended: false temp: name: temp required: false recommended: false - class_uri: MIXS:0016007 - HydrocarbonResourcesCores: - name: HydrocarbonResourcesCores - description: hydrocarbon resources-cores extension - title: hydrocarbon resources-cores + water_temp_regm: + name: water_temp_regm + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' + required: false + recommended: false + watering_regm: + name: watering_regm + string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' + required: false + recommended: false + class_uri: MIXS:0016010 + Sediment: + name: Sediment + description: sediment extension + title: sediment from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: - samp_name - project_name - - hcr - - hc_produced - - basin - - field - - reservoir - - hcr_temp - - tvdss_of_hcr_temp - - hcr_pressure - - tvdss_of_hcr_press - - permeability - - porosity - - lithology - - depos_env - - hcr_geol_age - - owc_tvdss - - hcr_fw_salinity - - sulfate_fw - - vfa_fw - - sr_kerog_type - - sr_lithology - - sr_dep_env - - sr_geol_age - - samp_well_name - - win - - samp_type - - samp_subtype - - temp - - pressure - - samp_tvdss - - samp_md + - depth - elev - - oxy_stat_samp - - samp_transport_cond - - samp_store_temp - - samp_store_dur - - samp_store_loc - - samp_vol_we_dna_ext - - organism_count - - org_count_qpcr_info - - ph - - salinity - alkalinity - - alkalinity_method - - sulfate - - sulfide - - tot_sulfur - - nitrate - - nitrite + - alkyl_diethers + - aminopept_act - ammonium - - tot_nitro - - diss_iron - - sodium - - chloride - - potassium - - magnesium + - bacteria_carb_prod + - biomass + - bishomohopanol + - bromide - calcium - - tot_iron - - diss_org_carb - - diss_inorg_carb - - diss_inorg_phosp - - tot_phosp - - suspend_solids + - carb_nitro_ratio + - chem_administration + - chloride + - chlorophyll - density + - diether_lipids - diss_carb_dioxide - - diss_oxygen_fluid - - vfa - - benzene - - toluene - - ethylbenzene - - xylene - - api - - tan - - viscosity - - pour_point - - saturates_pc - - aromatics_pc - - resins_pc - - asphaltenes_pc + - diss_hydrogen + - diss_inorg_carb + - diss_org_carb + - diss_org_nitro + - diss_oxygen + - glucosidase_act + - magnesium + - mean_frict_vel + - mean_peak_frict_vel + - methane - misc_param - - additional_info + - n_alkanes + - nitrate + - nitrite + - nitro + - org_carb + - org_matter + - org_nitro + - organism_count + - oxy_stat_samp + - ph + - particle_class + - part_org_carb + - perturbation + - petroleum_hydrocarb + - phaeopigments + - phosphate + - phosplipid_fatt_acid + - porosity + - potassium + - pressure + - redox_potential + - salinity + - samp_store_dur + - samp_store_loc + - samp_store_temp + - samp_vol_we_dna_ext + - sediment_type + - silicate + - sodium + - sulfate + - sulfide + - temp + - tidal_stage + - tot_carb + - tot_depth_water_col + - tot_nitro_content + - tot_org_carb + - turbidity + - water_content slot_usage: + alkyl_diethers: + name: alkyl_diethers ammonium: name: ammonium - recommended: true - depos_env: - name: depos_env - examples: - - value: Continental - Alluvial - diss_inorg_phosp: - name: diss_inorg_phosp - recommended: true - elev: - name: elev required: false recommended: false - hcr_temp: - name: hcr_temp + bacteria_carb_prod: + name: bacteria_carb_prod + chem_administration: + name: chem_administration + required: false + recommended: false + depth: + name: depth + examples: + - value: 10 meter required: true + diss_org_nitro: + name: diss_org_nitro + elev: + name: elev + recommended: true + methane: + name: methane + examples: + - value: 0.15 micromole per liter + n_alkanes: + name: n_alkanes nitrate: name: nitrate - recommended: true + required: false + recommended: false nitrite: name: nitrite - recommended: true + required: false + recommended: false + org_carb: + name: org_carb + org_nitro: + name: org_nitro organism_count: name: organism_count examples: - value: total prokaryotes;3.5e7 cells per milliliter;qPCR - recommended: true + required: false + recommended: false oxy_stat_samp: name: oxy_stat_samp required: false recommended: false + part_org_carb: + name: part_org_carb + perturbation: + name: perturbation + required: false + recommended: false ph: name: ph - recommended: true + required: false + recommended: false + phosplipid_fatt_acid: + name: phosplipid_fatt_acid samp_store_dur: name: samp_store_dur required: false @@ -23151,255 +26863,341 @@ classes: recommended: false samp_vol_we_dna_ext: name: samp_vol_we_dna_ext - recommended: true + required: false + recommended: false sulfate: name: sulfate - recommended: true - sulfate_fw: - name: sulfate_fw - required: true + required: false + recommended: false sulfide: name: sulfide - recommended: true + required: false + recommended: false temp: name: temp - required: true - vfa_fw: - name: vfa_fw - required: true - class_uri: MIXS:0016015 - HydrocarbonResourcesFluidsSwabs: - name: HydrocarbonResourcesFluidsSwabs - description: hydrocarbon resources-fluids/swabs extension - title: hydrocarbon resources-fluids/swabs + required: false + recommended: false + tot_carb: + name: tot_carb + required: false + recommended: false + tot_nitro_content: + name: tot_nitro_content + required: false + recommended: false + tot_org_carb: + name: tot_org_carb + required: false + recommended: false + turbidity: + name: turbidity + water_content: + name: water_content + string_serialization: '{float} {unit}' + class_uri: MIXS:0016011 + Soil: + name: Soil + description: soil extension + title: soil from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: - samp_name - project_name - - hcr - - hc_produced - - basin - - field - - reservoir - - hcr_temp - - tvdss_of_hcr_temp - - hcr_pressure - - tvdss_of_hcr_press - - lithology - - depos_env - - hcr_geol_age - - hcr_fw_salinity - - sulfate_fw - - vfa_fw - - prod_start_date - - prod_rate - - water_prod_rate - - water_cut - - iwf - - add_recov_method - - iw_bt_date_well - - biocide - - biocide_admin_method - - chem_treatment - - chem_treat_method - - samp_loc_corr_rate - - samp_well_name - - win - - samp_type - - samp_subtype - - samp_collect_point - - temp - - pressure - - oxy_stat_samp - - samp_preserv - - samp_transport_cond - - samp_store_temp - - samp_store_dur - - samp_store_loc + - depth + - elev + - cur_land_use + - cur_vegetation + - cur_vegetation_meth + - previous_land_use + - prev_land_use_meth + - crop_rotation + - agrochem_addition + - tillage + - fire + - flooding + - extreme_event + - soil_horizon + - horizon_meth + - sieving + - water_content + - water_cont_soil_meth - samp_vol_we_dna_ext - - organism_count - - org_count_qpcr_info + - pool_dna_extracts + - store_cond + - link_climate_info + - annual_temp + - season_temp + - annual_precpt + - season_precpt + - link_class_info + - fao_class + - local_class + - local_class_meth + - org_nitro + - temp + - soil_type + - soil_type_meth + - slope_gradient + - slope_aspect + - profile_position + - drainage_class + - soil_texture + - soil_texture_meth - ph - - salinity - - alkalinity - - alkalinity_method - - sulfate - - sulfide - - tot_sulfur - - nitrate - - nitrite - - ammonium - - tot_nitro - - diss_iron - - sodium - - chloride - - potassium - - magnesium - - calcium - - tot_iron - - diss_org_carb - - diss_inorg_carb - - diss_inorg_phosp - - tot_phosp - - suspend_solids - - density - - diss_carb_dioxide - - diss_oxygen_fluid - - vfa - - benzene - - toluene - - ethylbenzene - - xylene - - api - - tan - - viscosity - - pour_point - - saturates_pc - - aromatics_pc - - resins_pc - - asphaltenes_pc + - ph_meth + - org_matter + - tot_org_carb + - tot_org_c_meth + - tot_nitro_content + - tot_nitro_cont_meth + - microbial_biomass + - micro_biomass_meth + - link_addit_analys + - heavy_metals + - heavy_metals_meth + - al_sat + - al_sat_meth - misc_param - - additional_info slot_usage: - ammonium: - name: ammonium - recommended: true - depos_env: - name: depos_env + crop_rotation: + name: crop_rotation + string_serialization: '{boolean};{Rn/start_time/end_time/duration}' + required: false + recommended: false + cur_vegetation: + name: cur_vegetation + required: false + recommended: false + cur_vegetation_meth: + name: cur_vegetation_meth + required: false + recommended: false + depth: + name: depth examples: - - value: Marine - Reef - diss_inorg_phosp: - name: diss_inorg_phosp - recommended: true - hcr_temp: - name: hcr_temp - recommended: true - nitrate: - name: nitrate + - value: 10 meter required: true - nitrite: - name: nitrite - recommended: true - organism_count: - name: organism_count - examples: - - value: total prokaryotes;3.5e7 cells per milliliter;qPCR - recommended: true - oxy_stat_samp: - name: oxy_stat_samp + drainage_class: + name: drainage_class + required: false + recommended: false + elev: + name: elev + required: true + extreme_event: + name: extreme_event + required: false + recommended: false + fao_class: + name: fao_class + required: false + recommended: false + fire: + name: fire + required: false + recommended: false + flooding: + name: flooding + required: false + recommended: false + heavy_metals_meth: + name: heavy_metals_meth + string_serialization: '{PMID}|{DOI}|{URL}' + required: false + recommended: false + horizon_meth: + name: horizon_meth required: false recommended: false + local_class: + name: local_class + required: false + recommended: false + local_class_meth: + name: local_class_meth + required: false + recommended: false + micro_biomass_meth: + name: micro_biomass_meth + required: false + recommended: false + microbial_biomass: + name: microbial_biomass + required: false + recommended: false + org_nitro: + name: org_nitro ph: name: ph - recommended: true - samp_store_dur: - name: samp_store_dur required: false recommended: false - samp_store_loc: - name: samp_store_loc + ph_meth: + name: ph_meth + required: false + recommended: false + pool_dna_extracts: + name: pool_dna_extracts + string_serialization: '{boolean};{integer}' + required: false + recommended: false + prev_land_use_meth: + name: prev_land_use_meth + required: false + recommended: false + previous_land_use: + name: previous_land_use + required: false + recommended: false + profile_position: + name: profile_position required: false recommended: false samp_vol_we_dna_ext: name: samp_vol_we_dna_ext - recommended: true - sulfate: - name: sulfate - required: true - sulfate_fw: - name: sulfate_fw - recommended: true - sulfide: - name: sulfide - required: true + required: false + recommended: false + season_precpt: + name: season_precpt + sieving: + name: sieving + required: false + recommended: false + slope_aspect: + name: slope_aspect + required: false + recommended: false + slope_gradient: + name: slope_gradient + required: false + recommended: false + soil_horizon: + name: soil_horizon + required: false + recommended: false + soil_type: + name: soil_type + string_serialization: '{termLabel} [{termID}] + + ' + required: false + recommended: false + soil_type_meth: + name: soil_type_meth + required: false + recommended: false + store_cond: + name: store_cond + required: false + recommended: false temp: name: temp - required: true - vfa_fw: - name: vfa_fw - recommended: true - class_uri: MIXS:0016016 - MicrobialMatBiofilm: - name: MicrobialMatBiofilm - description: microbial mat/biofilm extension - title: microbial mat/biofilm + required: false + recommended: false + tillage: + name: tillage + required: false + recommended: false + tot_nitro_cont_meth: + name: tot_nitro_cont_meth + required: false + recommended: false + tot_nitro_content: + name: tot_nitro_content + required: false + recommended: false + tot_org_c_meth: + name: tot_org_c_meth + required: false + recommended: false + tot_org_carb: + name: tot_org_carb + required: false + recommended: false + water_content: + name: water_content + string_serialization: '{float}' + class_uri: MIXS:0016012 + SymbiontAssociated: + name: SymbiontAssociated + description: symbiont-associated extension + title: symbiont-associated from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: - samp_name - project_name + - lat_lon + - geo_loc_name + - collection_date + - alt - depth - elev - - alkalinity - - alkyl_diethers - - aminopept_act - - ammonium - - bacteria_carb_prod - - biomass - - bishomohopanol - - bromide - - calcium - - carb_nitro_ratio - - chem_administration - - chloride - - chlorophyll - - diether_lipids - - diss_carb_dioxide - - diss_hydrogen - - diss_inorg_carb - - diss_org_carb - - diss_org_nitro - - diss_oxygen - - glucosidase_act - - magnesium - - mean_frict_vel - - mean_peak_frict_vel - - methane - - misc_param - - n_alkanes - - nitrate - - nitrite - - nitro - - org_carb - - org_matter - - org_nitro - - organism_count - - oxy_stat_samp - - ph - - part_org_carb + - host_subject_id + - host_common_name + - host_taxid + - source_mat_id + - host_dependence + - type_of_symbiosis + - sym_life_cycle_type + - host_life_stage + - host_age + - urobiom_sex + - mode_transmission + - route_transmission + - host_body_habitat + - host_body_site + - host_body_product + - host_tot_mass + - host_height + - host_length + - host_growth_cond + - host_substrate + - host_fam_rel + - host_infra_spec_name + - host_infra_spec_rank + - host_genotype + - host_phenotype + - host_dry_mass + - host_color + - host_shape + - gravidity + - host_number + - host_symbiont + - host_specificity + - symbiont_host_role + - host_cellular_loc + - association_duration + - host_of_host_coinf + - host_of_host_name + - host_of_host_env_loc + - host_of_host_env_med + - host_of_host_taxid + - host_of_host_sub_id + - host_of_host_disease + - host_of_host_fam_rel + - host_of_host_infname + - host_of_host_infrank + - host_of_host_geno + - host_of_host_pheno + - host_of_host_gravid + - host_of_host_totmass + - chem_administration - perturbation - - petroleum_hydrocarb - - phaeopigments - - phosphate - - phosplipid_fatt_acid - - potassium - - pressure - - redox_potential - salinity + - oxy_stat_samp + - temp + - organism_count + - samp_vol_we_dna_ext + - samp_store_temp - samp_store_dur - samp_store_loc - - samp_store_temp - - samp_vol_we_dna_ext - - silicate - - sodium - - sulfate - - sulfide - - temp - - tot_carb - - tot_nitro_content - - tot_org_carb - - turbidity - - water_content + - samp_store_sol + - misc_param slot_usage: - alkyl_diethers: - name: alkyl_diethers - ammonium: - name: ammonium - required: false - recommended: false - bacteria_carb_prod: - name: bacteria_carb_prod + alt: + name: alt + recommended: true chem_administration: name: chem_administration required: false @@ -23409,29 +27207,83 @@ classes: examples: - value: 10 meter recommended: true - diss_org_nitro: - name: diss_org_nitro elev: name: elev recommended: true - methane: - name: methane + gravidity: + name: gravidity + host_age: + name: host_age + required: false + recommended: false + host_body_habitat: + name: host_body_habitat examples: - - value: 0.15 micromole per liter - n_alkanes: - name: n_alkanes - nitrate: - name: nitrate + - value: anterior end of a tapeworm + host_body_site: + name: host_body_site + examples: + - value: scolex [UBERON:0015119] + host_color: + name: host_color + host_common_name: + name: host_common_name + examples: + - value: trematode required: false recommended: false - nitrite: - name: nitrite + host_fam_rel: + name: host_fam_rel + examples: + - value: clone;P15 + host_genotype: + name: host_genotype + required: false + recommended: false + host_growth_cond: + name: host_growth_cond + host_height: + name: host_height + required: false + recommended: false + host_length: + name: host_length + required: false + recommended: false + host_life_stage: + name: host_life_stage + examples: + - value: redia + required: true + host_phenotype: + name: host_phenotype + examples: + - value: soldier + required: false + recommended: false + host_shape: + name: host_shape + host_subject_id: + name: host_subject_id + examples: + - value: P14 + host_substrate: + name: host_substrate + host_symbiont: + name: host_symbiont + examples: + - value: Paragordius varius + host_taxid: + name: host_taxid + examples: + - value: '395013' + string_serialization: '{integer}' + required: false + recommended: false + host_tot_mass: + name: host_tot_mass required: false recommended: false - org_carb: - name: org_carb - org_nitro: - name: org_nitro organism_count: name: organism_count examples: @@ -23442,18 +27294,10 @@ classes: name: oxy_stat_samp required: false recommended: false - part_org_carb: - name: part_org_carb perturbation: name: perturbation required: false recommended: false - ph: - name: ph - required: false - recommended: false - phosplipid_fatt_acid: - name: phosplipid_fatt_acid samp_store_dur: name: samp_store_dur required: false @@ -23466,97 +27310,63 @@ classes: name: samp_vol_we_dna_ext required: false recommended: false - sulfate: - name: sulfate - required: false - recommended: false - sulfide: - name: sulfide + source_mat_id: + name: source_mat_id required: false recommended: false temp: name: temp required: false recommended: false - tot_carb: - name: tot_carb - required: false - recommended: false - tot_nitro_content: - name: tot_nitro_content - required: false - recommended: false - tot_org_carb: - name: tot_org_carb - required: false - recommended: false - turbidity: - name: turbidity - water_content: - name: water_content - string_serialization: '{float} {unit}' - class_uri: MIXS:0016008 - MiscellaneousNaturalOrArtificialEnvironment: - name: MiscellaneousNaturalOrArtificialEnvironment - description: miscellaneous natural or artificial environment extension - title: miscellaneous natural or artificial environment + class_uri: MIXS:0016023 + WastewaterSludge: + name: WastewaterSludge + description: wastewater/sludge extension + title: wastewater/sludge from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: - samp_name - project_name - - alt - depth - - elev - alkalinity - - ammonium - - biomass - - bromide - - calcium + - biochem_oxygen_dem - chem_administration - - chloride - - chlorophyll - - density - - diether_lipids - - diss_carb_dioxide - - diss_hydrogen - - diss_inorg_carb - - diss_org_nitro - - diss_oxygen + - chem_oxygen_dem + - efficiency_percent + - emulsions + - gaseous_substances + - indust_eff_percent + - inorg_particles - misc_param - nitrate - - nitrite - - nitro - - org_carb - - org_matter - - org_nitro + - org_particles - organism_count - oxy_stat_samp - ph - perturbation - phosphate - - phosplipid_fatt_acid - - potassium - - pressure + - pre_treatment + - primary_treatment + - reactor_type - salinity - samp_store_dur - samp_store_loc - samp_store_temp - samp_vol_we_dna_ext - - silicate + - secondary_treatment + - sewage_type + - sludge_retent_time - sodium - - sulfate - - sulfide + - soluble_inorg_mat + - soluble_org_mat + - suspend_solids - temp - - water_current + - tertiary_treatment + - tot_nitro + - tot_phosphate + - wastewater_type slot_usage: - alt: - name: alt - recommended: true - ammonium: - name: ammonium - required: false - recommended: false chem_administration: name: chem_administration required: false @@ -23565,24 +27375,11 @@ classes: name: depth examples: - value: 10 meter - recommended: true - diss_org_nitro: - name: diss_org_nitro - elev: - name: elev - recommended: true - nitrate: - name: nitrate - required: false - recommended: false - nitrite: - name: nitrite + recommended: true + nitrate: + name: nitrate required: false recommended: false - org_carb: - name: org_carb - org_nitro: - name: org_nitro organism_count: name: organism_count examples: @@ -23601,8 +27398,6 @@ classes: name: ph required: false recommended: false - phosplipid_fatt_acid: - name: phosplipid_fatt_acid samp_store_dur: name: samp_store_dur required: false @@ -23615,23 +27410,19 @@ classes: name: samp_vol_we_dna_ext required: false recommended: false - sulfate: - name: sulfate - required: false - recommended: false - sulfide: - name: sulfide - required: false - recommended: false temp: name: temp required: false recommended: false - class_uri: MIXS:0016009 - PlantAssociated: - name: PlantAssociated - description: plant-associated extension - title: plant-associated + tot_phosphate: + name: tot_phosphate + required: false + recommended: false + class_uri: MIXS:0016013 + Water: + name: Water + description: water extension + title: water from_schema: https://w3id.org/mixs-6-2-rc is_a: Extension slots: @@ -23639,182 +27430,128 @@ classes: - project_name - depth - elev - - air_temp_regm - - ances_data - - antibiotic_regm - - biol_stat - - biotic_regm + - alkalinity + - alkalinity_method + - alkyl_diethers + - aminopept_act + - ammonium + - atmospheric_data + - bacteria_carb_prod + - bac_prod + - bac_resp + - biomass + - bishomohopanol + - bromide + - calcium + - carb_nitro_ratio - chem_administration - - chem_mutagen - - climate_environment - - cult_root_med - - fertilizer_regm - - fungicide_regm - - gaseous_environment - - genetic_mod - - gravity - - growth_facil - - growth_habit - - growth_hormone_regm - - herbicide_regm - - host_age - - host_common_name - - host_disease_stat - - host_dry_mass - - host_genotype - - host_height - - host_subspecf_genlin - - host_length - - host_life_stage - - host_phenotype - - host_taxid - - host_tot_mass - - host_wet_mass - - humidity_regm - - light_regm - - mechanical_damage - - mineral_nutr_regm + - chloride + - chlorophyll + - conduc + - density + - diether_lipids + - diss_carb_dioxide + - diss_hydrogen + - diss_inorg_carb + - diss_inorg_nitro + - diss_inorg_phosp + - diss_org_carb + - diss_org_nitro + - diss_oxygen + - down_par + - fluor + - glucosidase_act + - light_intensity + - magnesium + - mean_frict_vel + - mean_peak_frict_vel - misc_param - - non_min_nutr_regm + - n_alkanes + - nitrate + - nitrite + - nitro + - org_carb + - org_matter + - org_nitro - organism_count - oxy_stat_samp - - ph_regm + - ph + - part_org_carb + - part_org_nitro - perturbation - - pesticide_regm - - plant_growth_med - - plant_product - - plant_sex - - plant_struc - - radiation_regm - - rainfall_regm - - root_cond - - root_med_carbon - - root_med_macronutr - - root_med_micronutr - - root_med_suppl - - root_med_ph - - root_med_regl - - root_med_solid - - salt_regm - - samp_capt_status - - samp_dis_stage + - petroleum_hydrocarb + - phaeopigments + - phosphate + - phosplipid_fatt_acid + - photon_flux + - potassium + - pressure + - primary_prod + - redox_potential - salinity - samp_store_dur - samp_store_loc - samp_store_temp - samp_vol_we_dna_ext - - season_environment - - standing_water_regm + - silicate + - size_frac_low + - size_frac_up + - sodium + - soluble_react_phosp + - sulfate + - sulfide + - suspend_part_matter - temp - - tiss_cult_growth_med - - water_temp_regm - - watering_regm - - host_symbiont + - tidal_stage + - tot_depth_water_col + - tot_diss_nitro + - tot_inorg_nitro + - tot_nitro + - tot_part_carb + - tot_phosp + - turbidity + - water_current slot_usage: - biotic_regm: - name: biotic_regm + alkyl_diethers: + name: alkyl_diethers + ammonium: + name: ammonium required: false recommended: false + bacteria_carb_prod: + name: bacteria_carb_prod chem_administration: name: chem_administration required: false recommended: false - climate_environment: - name: climate_environment - string_serialization: '{text};{Rn/start_time/end_time/duration}' - required: false - recommended: false depth: name: depth examples: - value: 10 meter - recommended: true - elev: - name: elev - recommended: true - fungicide_regm: - name: fungicide_regm - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - required: false - recommended: false - gaseous_environment: - name: gaseous_environment - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - required: false - recommended: false - herbicide_regm: - name: herbicide_regm - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - required: false - recommended: false - host_age: - name: host_age - examples: - - value: 10 days - required: false - recommended: false - host_common_name: - name: host_common_name - examples: - - value: rice - required: false - recommended: false - host_disease_stat: - name: host_disease_stat - examples: - - value: downy mildew - required: false - recommended: false - host_genotype: - name: host_genotype - examples: - - value: Ts - required: false - recommended: false - host_height: - name: host_height - examples: - - value: 1 meter - required: false - recommended: false - host_length: - name: host_length - required: false - recommended: false - host_life_stage: - name: host_life_stage - examples: - - value: adult - required: false - recommended: false - host_phenotype: - name: host_phenotype - examples: - - value: seed pod; green [PATO:0000320] - required: false - recommended: false - host_symbiont: - name: host_symbiont - examples: - - value: flukeworms - host_taxid: - name: host_taxid - examples: - - value: '4530' - string_serialization: '{NCBI taxid}' - required: false - recommended: false - host_tot_mass: - name: host_tot_mass - examples: - - value: 2500 gram + required: true + diss_inorg_phosp: + name: diss_inorg_phosp required: false recommended: false - non_min_nutr_regm: - name: non_min_nutr_regm - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + diss_org_nitro: + name: diss_org_nitro + elev: + name: elev + recommended: true + n_alkanes: + name: n_alkanes + nitrate: + name: nitrate + required: false + recommended: false + nitrite: + name: nitrite required: false recommended: false + org_carb: + name: org_carb + org_nitro: + name: org_nitro organism_count: name: organism_count examples: @@ -23825,37 +27562,18 @@ classes: name: oxy_stat_samp required: false recommended: false + part_org_carb: + name: part_org_carb perturbation: name: perturbation required: false recommended: false - pesticide_regm: - name: pesticide_regm - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' - required: false - recommended: false - ph_regm: - name: ph_regm - string_serialization: '{float};{Rn/start_time/end_time/duration}' - required: false - recommended: false - plant_growth_med: - name: plant_growth_med - examples: - - value: hydroponic plant culture media [EO:0007067] - plant_product: - name: plant_product - required: false - recommended: false - plant_struc: - name: plant_struc - required: false - recommended: false - salt_regm: - name: salt_regm - string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' + ph: + name: ph required: false recommended: false + phosplipid_fatt_acid: + name: phosplipid_fatt_acid samp_store_dur: name: samp_store_dur required: false @@ -23868,1218 +27586,3336 @@ classes: name: samp_vol_we_dna_ext required: false recommended: false - season_environment: - name: season_environment - string_serialization: '{text};{Rn/start_time/end_time/duration}' + sulfate: + name: sulfate required: false recommended: false - standing_water_regm: - name: standing_water_regm - string_serialization: '{text};{Rn/start_time/end_time/duration}' + sulfide: + name: sulfide required: false recommended: false temp: name: temp required: false recommended: false - water_temp_regm: - name: water_temp_regm - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' - required: false - recommended: false - watering_regm: - name: watering_regm - string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' - required: false - recommended: false - class_uri: MIXS:0016010 - Sediment: - name: Sediment - description: sediment extension - title: sediment + turbidity: + name: turbidity + class_uri: MIXS:0016014 + Checklist: + name: Checklist + description: A collection of metadata terms (slots) to minimally describe the + sampling and sequencing method of a specimen used to generate a nucleotide sequence. + from_schema: https://w3id.org/mixs-6-2-rc + Extension: + name: Extension + description: A collection of recommended metadata terms (slots) developed by community + experts, describing the specific context under which a sample was collected. + from_schema: https://w3id.org/mixs-6-2-rc + aliases: + - EnvironmentalPackage + MixsCompliantData: + name: MixsCompliantData + description: A collection of data that complies with some combination of a MIxS + checklist and environmental extension + title: MIxS compliant data + from_schema: https://w3id.org/mixs-6-2-rc + slots: + - migs_ba_data + - agriculture_data + - migs_ba_agriculture_data + - air_data + - migs_ba_air_data + - built_environment_data + - migs_ba_built_environment_data + - food_animal_and_animal_feed_data + - migs_ba_food_animal_and_animal_feed_data + - food_farm_environment_data + - migs_ba_food_farm_environment_data + - food_food_production_facility_data + - migs_ba_food_food_production_facility_data + - food_human_foods_data + - migs_ba_food_human_foods_data + - host_associated_data + - migs_ba_host_associated_data + - human_associated_data + - migs_ba_human_associated_data + - human_gut_data + - migs_ba_human_gut_data + - human_oral_data + - migs_ba_human_oral_data + - human_skin_data + - migs_ba_human_skin_data + - human_vaginal_data + - migs_ba_human_vaginal_data + - hydrocarbon_resources_cores_data + - migs_ba_hydrocarbon_resources_cores_data + - hydrocarbon_resources_fluids_swabs_data + - migs_ba_hydrocarbon_resources_fluids_swabs_data + - microbial_mat_biofilm_data + - migs_ba_microbial_mat_biofilm_data + - miscellaneous_natural_or_artificial_environment_data + - migs_ba_miscellaneous_natural_or_artificial_environment_data + - plant_associated_data + - migs_ba_plant_associated_data + - sediment_data + - migs_ba_sediment_data + - soil_data + - migs_ba_soil_data + - symbiont_associated_data + - migs_ba_symbiont_associated_data + - wastewater_sludge_data + - migs_ba_wastewater_sludge_data + - water_data + - migs_ba_water_data + - migs_eu_data + - migs_eu_agriculture_data + - migs_eu_air_data + - migs_eu_built_environment_data + - migs_eu_food_animal_and_animal_feed_data + - migs_eu_food_farm_environment_data + - migs_eu_food_food_production_facility_data + - migs_eu_food_human_foods_data + - migs_eu_host_associated_data + - migs_eu_human_associated_data + - migs_eu_human_gut_data + - migs_eu_human_oral_data + - migs_eu_human_skin_data + - migs_eu_human_vaginal_data + - migs_eu_hydrocarbon_resources_cores_data + - migs_eu_hydrocarbon_resources_fluids_swabs_data + - migs_eu_microbial_mat_biofilm_data + - migs_eu_miscellaneous_natural_or_artificial_environment_data + - migs_eu_plant_associated_data + - migs_eu_sediment_data + - migs_eu_soil_data + - migs_eu_symbiont_associated_data + - migs_eu_wastewater_sludge_data + - migs_eu_water_data + - migs_org_data + - migs_org_agriculture_data + - migs_org_air_data + - migs_org_built_environment_data + - migs_org_food_animal_and_animal_feed_data + - migs_org_food_farm_environment_data + - migs_org_food_food_production_facility_data + - migs_org_food_human_foods_data + - migs_org_host_associated_data + - migs_org_human_associated_data + - migs_org_human_gut_data + - migs_org_human_oral_data + - migs_org_human_skin_data + - migs_org_human_vaginal_data + - migs_org_hydrocarbon_resources_cores_data + - migs_org_hydrocarbon_resources_fluids_swabs_data + - migs_org_microbial_mat_biofilm_data + - migs_org_miscellaneous_natural_or_artificial_environment_data + - migs_org_plant_associated_data + - migs_org_sediment_data + - migs_org_soil_data + - migs_org_symbiont_associated_data + - migs_org_wastewater_sludge_data + - migs_org_water_data + - migs_pl_data + - migs_pl_agriculture_data + - migs_pl_air_data + - migs_pl_built_environment_data + - migs_pl_food_animal_and_animal_feed_data + - migs_pl_food_farm_environment_data + - migs_pl_food_food_production_facility_data + - migs_pl_food_human_foods_data + - migs_pl_host_associated_data + - migs_pl_human_associated_data + - migs_pl_human_gut_data + - migs_pl_human_oral_data + - migs_pl_human_skin_data + - migs_pl_human_vaginal_data + - migs_pl_hydrocarbon_resources_cores_data + - migs_pl_hydrocarbon_resources_fluids_swabs_data + - migs_pl_microbial_mat_biofilm_data + - migs_pl_miscellaneous_natural_or_artificial_environment_data + - migs_pl_plant_associated_data + - migs_pl_sediment_data + - migs_pl_soil_data + - migs_pl_symbiont_associated_data + - migs_pl_wastewater_sludge_data + - migs_pl_water_data + - migs_vi_data + - migs_vi_agriculture_data + - migs_vi_air_data + - migs_vi_built_environment_data + - migs_vi_food_animal_and_animal_feed_data + - migs_vi_food_farm_environment_data + - migs_vi_food_food_production_facility_data + - migs_vi_food_human_foods_data + - migs_vi_host_associated_data + - migs_vi_human_associated_data + - migs_vi_human_gut_data + - migs_vi_human_oral_data + - migs_vi_human_skin_data + - migs_vi_human_vaginal_data + - migs_vi_hydrocarbon_resources_cores_data + - migs_vi_hydrocarbon_resources_fluids_swabs_data + - migs_vi_microbial_mat_biofilm_data + - migs_vi_miscellaneous_natural_or_artificial_environment_data + - migs_vi_plant_associated_data + - migs_vi_sediment_data + - migs_vi_soil_data + - migs_vi_symbiont_associated_data + - migs_vi_wastewater_sludge_data + - migs_vi_water_data + - mimag_data + - mimag_agriculture_data + - mimag_air_data + - mimag_built_environment_data + - mimag_food_animal_and_animal_feed_data + - mimag_food_farm_environment_data + - mimag_food_food_production_facility_data + - mimag_food_human_foods_data + - mimag_host_associated_data + - mimag_human_associated_data + - mimag_human_gut_data + - mimag_human_oral_data + - mimag_human_skin_data + - mimag_human_vaginal_data + - mimag_hydrocarbon_resources_cores_data + - mimag_hydrocarbon_resources_fluids_swabs_data + - mimag_microbial_mat_biofilm_data + - mimag_miscellaneous_natural_or_artificial_environment_data + - mimag_plant_associated_data + - mimag_sediment_data + - mimag_soil_data + - mimag_symbiont_associated_data + - mimag_wastewater_sludge_data + - mimag_water_data + - mimarks_c_data + - mimarks_c_agriculture_data + - mimarks_c_air_data + - mimarks_c_built_environment_data + - mimarks_c_food_animal_and_animal_feed_data + - mimarks_c_food_farm_environment_data + - mimarks_c_food_food_production_facility_data + - mimarks_c_food_human_foods_data + - mimarks_c_host_associated_data + - mimarks_c_human_associated_data + - mimarks_c_human_gut_data + - mimarks_c_human_oral_data + - mimarks_c_human_skin_data + - mimarks_c_human_vaginal_data + - mimarks_c_hydrocarbon_resources_cores_data + - mimarks_c_hydrocarbon_resources_fluids_swabs_data + - mimarks_c_microbial_mat_biofilm_data + - mimarks_c_miscellaneous_natural_or_artificial_environment_data + - mimarks_c_plant_associated_data + - mimarks_c_sediment_data + - mimarks_c_soil_data + - mimarks_c_symbiont_associated_data + - mimarks_c_wastewater_sludge_data + - mimarks_c_water_data + - mimarks_s_data + - mimarks_s_agriculture_data + - mimarks_s_air_data + - mimarks_s_built_environment_data + - mimarks_s_food_animal_and_animal_feed_data + - mimarks_s_food_farm_environment_data + - mimarks_s_food_food_production_facility_data + - mimarks_s_food_human_foods_data + - mimarks_s_host_associated_data + - mimarks_s_human_associated_data + - mimarks_s_human_gut_data + - mimarks_s_human_oral_data + - mimarks_s_human_skin_data + - mimarks_s_human_vaginal_data + - mimarks_s_hydrocarbon_resources_cores_data + - mimarks_s_hydrocarbon_resources_fluids_swabs_data + - mimarks_s_microbial_mat_biofilm_data + - mimarks_s_miscellaneous_natural_or_artificial_environment_data + - mimarks_s_plant_associated_data + - mimarks_s_sediment_data + - mimarks_s_soil_data + - mimarks_s_symbiont_associated_data + - mimarks_s_wastewater_sludge_data + - mimarks_s_water_data + - mims_data + - mims_agriculture_data + - mims_air_data + - mims_built_environment_data + - mims_food_animal_and_animal_feed_data + - mims_food_farm_environment_data + - mims_food_food_production_facility_data + - mims_food_human_foods_data + - mims_host_associated_data + - mims_human_associated_data + - mims_human_gut_data + - mims_human_oral_data + - mims_human_skin_data + - mims_human_vaginal_data + - mims_hydrocarbon_resources_cores_data + - mims_hydrocarbon_resources_fluids_swabs_data + - mims_microbial_mat_biofilm_data + - mims_miscellaneous_natural_or_artificial_environment_data + - mims_plant_associated_data + - mims_sediment_data + - mims_soil_data + - mims_symbiont_associated_data + - mims_wastewater_sludge_data + - mims_water_data + - misag_data + - misag_agriculture_data + - misag_air_data + - misag_built_environment_data + - misag_food_animal_and_animal_feed_data + - misag_food_farm_environment_data + - misag_food_food_production_facility_data + - misag_food_human_foods_data + - misag_host_associated_data + - misag_human_associated_data + - misag_human_gut_data + - misag_human_oral_data + - misag_human_skin_data + - misag_human_vaginal_data + - misag_hydrocarbon_resources_cores_data + - misag_hydrocarbon_resources_fluids_swabs_data + - misag_microbial_mat_biofilm_data + - misag_miscellaneous_natural_or_artificial_environment_data + - misag_plant_associated_data + - misag_sediment_data + - misag_soil_data + - misag_symbiont_associated_data + - misag_wastewater_sludge_data + - misag_water_data + - miuvig_data + - miuvig_agriculture_data + - miuvig_air_data + - miuvig_built_environment_data + - miuvig_food_animal_and_animal_feed_data + - miuvig_food_farm_environment_data + - miuvig_food_food_production_facility_data + - miuvig_food_human_foods_data + - miuvig_host_associated_data + - miuvig_human_associated_data + - miuvig_human_gut_data + - miuvig_human_oral_data + - miuvig_human_skin_data + - miuvig_human_vaginal_data + - miuvig_hydrocarbon_resources_cores_data + - miuvig_hydrocarbon_resources_fluids_swabs_data + - miuvig_microbial_mat_biofilm_data + - miuvig_miscellaneous_natural_or_artificial_environment_data + - miuvig_plant_associated_data + - miuvig_sediment_data + - miuvig_soil_data + - miuvig_symbiont_associated_data + - miuvig_wastewater_sludge_data + - miuvig_water_data + tree_root: true + MigsBaAgriculture: + name: MigsBaAgriculture + description: MIxS data that complies with the MigsBa checklist and the Agriculture + Extension + title: MigsBa combined with Agriculture + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Agriculture + mixins: + - MigsBa + class_uri: MIXS:0010003_0016018 + MigsBaAir: + name: MigsBaAir + description: MIxS data that complies with the MigsBa checklist and the Air Extension + title: MigsBa combined with Air + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Air + mixins: + - MigsBa + class_uri: MIXS:0010003_0016000 + MigsBaBuiltEnvironment: + name: MigsBaBuiltEnvironment + description: MIxS data that complies with the MigsBa checklist and the BuiltEnvironment + Extension + title: MigsBa combined with BuiltEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: BuiltEnvironment + mixins: + - MigsBa + class_uri: MIXS:0010003_0016001 + MigsBaFoodAnimalAndAnimalFeed: + name: MigsBaFoodAnimalAndAnimalFeed + description: MIxS data that complies with the MigsBa checklist and the FoodAnimalAndAnimalFeed + Extension + title: MigsBa combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodAnimalAndAnimalFeed + mixins: + - MigsBa + class_uri: MIXS:0010003_0016019 + MigsBaFoodFarmEnvironment: + name: MigsBaFoodFarmEnvironment + description: MIxS data that complies with the MigsBa checklist and the FoodFarmEnvironment + Extension + title: MigsBa combined with FoodFarmEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFarmEnvironment + mixins: + - MigsBa + class_uri: MIXS:0010003_0016020 + MigsBaFoodFoodProductionFacility: + name: MigsBaFoodFoodProductionFacility + description: MIxS data that complies with the MigsBa checklist and the FoodFoodProductionFacility + Extension + title: MigsBa combined with FoodFoodProductionFacility + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFoodProductionFacility + mixins: + - MigsBa + class_uri: MIXS:0010003_0016021 + MigsBaFoodHumanFoods: + name: MigsBaFoodHumanFoods + description: MIxS data that complies with the MigsBa checklist and the FoodHumanFoods + Extension + title: MigsBa combined with FoodHumanFoods + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodHumanFoods + mixins: + - MigsBa + class_uri: MIXS:0010003_0016022 + MigsBaHostAssociated: + name: MigsBaHostAssociated + description: MIxS data that complies with the MigsBa checklist and the HostAssociated + Extension + title: MigsBa combined with HostAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HostAssociated + mixins: + - MigsBa + class_uri: MIXS:0010003_0016002 + MigsBaHumanAssociated: + name: MigsBaHumanAssociated + description: MIxS data that complies with the MigsBa checklist and the HumanAssociated + Extension + title: MigsBa combined with HumanAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanAssociated + mixins: + - MigsBa + class_uri: MIXS:0010003_0016003 + MigsBaHumanGut: + name: MigsBaHumanGut + description: MIxS data that complies with the MigsBa checklist and the HumanGut + Extension + title: MigsBa combined with HumanGut + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanGut + mixins: + - MigsBa + class_uri: MIXS:0010003_0016004 + MigsBaHumanOral: + name: MigsBaHumanOral + description: MIxS data that complies with the MigsBa checklist and the HumanOral + Extension + title: MigsBa combined with HumanOral + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanOral + mixins: + - MigsBa + class_uri: MIXS:0010003_0016005 + MigsBaHumanSkin: + name: MigsBaHumanSkin + description: MIxS data that complies with the MigsBa checklist and the HumanSkin + Extension + title: MigsBa combined with HumanSkin + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanSkin + mixins: + - MigsBa + class_uri: MIXS:0010003_0016006 + MigsBaHumanVaginal: + name: MigsBaHumanVaginal + description: MIxS data that complies with the MigsBa checklist and the HumanVaginal + Extension + title: MigsBa combined with HumanVaginal + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanVaginal + mixins: + - MigsBa + class_uri: MIXS:0010003_0016007 + MigsBaHydrocarbonResourcesCores: + name: MigsBaHydrocarbonResourcesCores + description: MIxS data that complies with the MigsBa checklist and the HydrocarbonResourcesCores + Extension + title: MigsBa combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesCores + mixins: + - MigsBa + class_uri: MIXS:0010003_0016015 + MigsBaHydrocarbonResourcesFluidsSwabs: + name: MigsBaHydrocarbonResourcesFluidsSwabs + description: MIxS data that complies with the MigsBa checklist and the HydrocarbonResourcesFluidsSwabs + Extension + title: MigsBa combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - MigsBa + class_uri: MIXS:0010003_0016016 + MigsBaMicrobialMatBiofilm: + name: MigsBaMicrobialMatBiofilm + description: MIxS data that complies with the MigsBa checklist and the MicrobialMatBiofilm + Extension + title: MigsBa combined with MicrobialMatBiofilm + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MicrobialMatBiofilm + mixins: + - MigsBa + class_uri: MIXS:0010003_0016008 + MigsBaMiscellaneousNaturalOrArtificialEnvironment: + name: MigsBaMiscellaneousNaturalOrArtificialEnvironment + description: MIxS data that complies with the MigsBa checklist and the MiscellaneousNaturalOrArtificialEnvironment + Extension + title: MigsBa combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - MigsBa + class_uri: MIXS:0010003_0016009 + MigsBaPlantAssociated: + name: MigsBaPlantAssociated + description: MIxS data that complies with the MigsBa checklist and the PlantAssociated + Extension + title: MigsBa combined with PlantAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: PlantAssociated + mixins: + - MigsBa + class_uri: MIXS:0010003_0016010 + MigsBaSediment: + name: MigsBaSediment + description: MIxS data that complies with the MigsBa checklist and the Sediment + Extension + title: MigsBa combined with Sediment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Sediment + mixins: + - MigsBa + class_uri: MIXS:0010003_0016011 + MigsBaSoil: + name: MigsBaSoil + description: MIxS data that complies with the MigsBa checklist and the Soil Extension + title: MigsBa combined with Soil + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Soil + mixins: + - MigsBa + class_uri: MIXS:0010003_0016012 + MigsBaSymbiontAssociated: + name: MigsBaSymbiontAssociated + description: MIxS data that complies with the MigsBa checklist and the SymbiontAssociated + Extension + title: MigsBa combined with SymbiontAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: SymbiontAssociated + mixins: + - MigsBa + class_uri: MIXS:0010003_0016023 + MigsBaWastewaterSludge: + name: MigsBaWastewaterSludge + description: MIxS data that complies with the MigsBa checklist and the WastewaterSludge + Extension + title: MigsBa combined with WastewaterSludge + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: WastewaterSludge + mixins: + - MigsBa + class_uri: MIXS:0010003_0016013 + MigsBaWater: + name: MigsBaWater + description: MIxS data that complies with the MigsBa checklist and the Water Extension + title: MigsBa combined with Water + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Water + mixins: + - MigsBa + class_uri: MIXS:0010003_0016014 + MigsEuAgriculture: + name: MigsEuAgriculture + description: MIxS data that complies with the MigsEu checklist and the Agriculture + Extension + title: MigsEu combined with Agriculture + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Agriculture + mixins: + - MigsEu + class_uri: MIXS:0010002_0016018 + MigsEuAir: + name: MigsEuAir + description: MIxS data that complies with the MigsEu checklist and the Air Extension + title: MigsEu combined with Air + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Air + mixins: + - MigsEu + class_uri: MIXS:0010002_0016000 + MigsEuBuiltEnvironment: + name: MigsEuBuiltEnvironment + description: MIxS data that complies with the MigsEu checklist and the BuiltEnvironment + Extension + title: MigsEu combined with BuiltEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: BuiltEnvironment + mixins: + - MigsEu + class_uri: MIXS:0010002_0016001 + MigsEuFoodAnimalAndAnimalFeed: + name: MigsEuFoodAnimalAndAnimalFeed + description: MIxS data that complies with the MigsEu checklist and the FoodAnimalAndAnimalFeed + Extension + title: MigsEu combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodAnimalAndAnimalFeed + mixins: + - MigsEu + class_uri: MIXS:0010002_0016019 + MigsEuFoodFarmEnvironment: + name: MigsEuFoodFarmEnvironment + description: MIxS data that complies with the MigsEu checklist and the FoodFarmEnvironment + Extension + title: MigsEu combined with FoodFarmEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFarmEnvironment + mixins: + - MigsEu + class_uri: MIXS:0010002_0016020 + MigsEuFoodFoodProductionFacility: + name: MigsEuFoodFoodProductionFacility + description: MIxS data that complies with the MigsEu checklist and the FoodFoodProductionFacility + Extension + title: MigsEu combined with FoodFoodProductionFacility + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFoodProductionFacility + mixins: + - MigsEu + class_uri: MIXS:0010002_0016021 + MigsEuFoodHumanFoods: + name: MigsEuFoodHumanFoods + description: MIxS data that complies with the MigsEu checklist and the FoodHumanFoods + Extension + title: MigsEu combined with FoodHumanFoods + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodHumanFoods + mixins: + - MigsEu + class_uri: MIXS:0010002_0016022 + MigsEuHostAssociated: + name: MigsEuHostAssociated + description: MIxS data that complies with the MigsEu checklist and the HostAssociated + Extension + title: MigsEu combined with HostAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HostAssociated + mixins: + - MigsEu + class_uri: MIXS:0010002_0016002 + MigsEuHumanAssociated: + name: MigsEuHumanAssociated + description: MIxS data that complies with the MigsEu checklist and the HumanAssociated + Extension + title: MigsEu combined with HumanAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanAssociated + mixins: + - MigsEu + class_uri: MIXS:0010002_0016003 + MigsEuHumanGut: + name: MigsEuHumanGut + description: MIxS data that complies with the MigsEu checklist and the HumanGut + Extension + title: MigsEu combined with HumanGut + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanGut + mixins: + - MigsEu + class_uri: MIXS:0010002_0016004 + MigsEuHumanOral: + name: MigsEuHumanOral + description: MIxS data that complies with the MigsEu checklist and the HumanOral + Extension + title: MigsEu combined with HumanOral + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanOral + mixins: + - MigsEu + class_uri: MIXS:0010002_0016005 + MigsEuHumanSkin: + name: MigsEuHumanSkin + description: MIxS data that complies with the MigsEu checklist and the HumanSkin + Extension + title: MigsEu combined with HumanSkin + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanSkin + mixins: + - MigsEu + class_uri: MIXS:0010002_0016006 + MigsEuHumanVaginal: + name: MigsEuHumanVaginal + description: MIxS data that complies with the MigsEu checklist and the HumanVaginal + Extension + title: MigsEu combined with HumanVaginal + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanVaginal + mixins: + - MigsEu + class_uri: MIXS:0010002_0016007 + MigsEuHydrocarbonResourcesCores: + name: MigsEuHydrocarbonResourcesCores + description: MIxS data that complies with the MigsEu checklist and the HydrocarbonResourcesCores + Extension + title: MigsEu combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesCores + mixins: + - MigsEu + class_uri: MIXS:0010002_0016015 + MigsEuHydrocarbonResourcesFluidsSwabs: + name: MigsEuHydrocarbonResourcesFluidsSwabs + description: MIxS data that complies with the MigsEu checklist and the HydrocarbonResourcesFluidsSwabs + Extension + title: MigsEu combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - MigsEu + class_uri: MIXS:0010002_0016016 + MigsEuMicrobialMatBiofilm: + name: MigsEuMicrobialMatBiofilm + description: MIxS data that complies with the MigsEu checklist and the MicrobialMatBiofilm + Extension + title: MigsEu combined with MicrobialMatBiofilm + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MicrobialMatBiofilm + mixins: + - MigsEu + class_uri: MIXS:0010002_0016008 + MigsEuMiscellaneousNaturalOrArtificialEnvironment: + name: MigsEuMiscellaneousNaturalOrArtificialEnvironment + description: MIxS data that complies with the MigsEu checklist and the MiscellaneousNaturalOrArtificialEnvironment + Extension + title: MigsEu combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - MigsEu + class_uri: MIXS:0010002_0016009 + MigsEuPlantAssociated: + name: MigsEuPlantAssociated + description: MIxS data that complies with the MigsEu checklist and the PlantAssociated + Extension + title: MigsEu combined with PlantAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: PlantAssociated + mixins: + - MigsEu + class_uri: MIXS:0010002_0016010 + MigsEuSediment: + name: MigsEuSediment + description: MIxS data that complies with the MigsEu checklist and the Sediment + Extension + title: MigsEu combined with Sediment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Sediment + mixins: + - MigsEu + class_uri: MIXS:0010002_0016011 + MigsEuSoil: + name: MigsEuSoil + description: MIxS data that complies with the MigsEu checklist and the Soil Extension + title: MigsEu combined with Soil + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Soil + mixins: + - MigsEu + class_uri: MIXS:0010002_0016012 + MigsEuSymbiontAssociated: + name: MigsEuSymbiontAssociated + description: MIxS data that complies with the MigsEu checklist and the SymbiontAssociated + Extension + title: MigsEu combined with SymbiontAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: SymbiontAssociated + mixins: + - MigsEu + class_uri: MIXS:0010002_0016023 + MigsEuWastewaterSludge: + name: MigsEuWastewaterSludge + description: MIxS data that complies with the MigsEu checklist and the WastewaterSludge + Extension + title: MigsEu combined with WastewaterSludge + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: WastewaterSludge + mixins: + - MigsEu + class_uri: MIXS:0010002_0016013 + MigsEuWater: + name: MigsEuWater + description: MIxS data that complies with the MigsEu checklist and the Water Extension + title: MigsEu combined with Water + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Water + mixins: + - MigsEu + class_uri: MIXS:0010002_0016014 + MigsOrgAgriculture: + name: MigsOrgAgriculture + description: MIxS data that complies with the MigsOrg checklist and the Agriculture + Extension + title: MigsOrg combined with Agriculture + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Agriculture + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016018 + MigsOrgAir: + name: MigsOrgAir + description: MIxS data that complies with the MigsOrg checklist and the Air Extension + title: MigsOrg combined with Air + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Air + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016000 + MigsOrgBuiltEnvironment: + name: MigsOrgBuiltEnvironment + description: MIxS data that complies with the MigsOrg checklist and the BuiltEnvironment + Extension + title: MigsOrg combined with BuiltEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: BuiltEnvironment + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016001 + MigsOrgFoodAnimalAndAnimalFeed: + name: MigsOrgFoodAnimalAndAnimalFeed + description: MIxS data that complies with the MigsOrg checklist and the FoodAnimalAndAnimalFeed + Extension + title: MigsOrg combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodAnimalAndAnimalFeed + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016019 + MigsOrgFoodFarmEnvironment: + name: MigsOrgFoodFarmEnvironment + description: MIxS data that complies with the MigsOrg checklist and the FoodFarmEnvironment + Extension + title: MigsOrg combined with FoodFarmEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFarmEnvironment + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016020 + MigsOrgFoodFoodProductionFacility: + name: MigsOrgFoodFoodProductionFacility + description: MIxS data that complies with the MigsOrg checklist and the FoodFoodProductionFacility + Extension + title: MigsOrg combined with FoodFoodProductionFacility + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFoodProductionFacility + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016021 + MigsOrgFoodHumanFoods: + name: MigsOrgFoodHumanFoods + description: MIxS data that complies with the MigsOrg checklist and the FoodHumanFoods + Extension + title: MigsOrg combined with FoodHumanFoods + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodHumanFoods + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016022 + MigsOrgHostAssociated: + name: MigsOrgHostAssociated + description: MIxS data that complies with the MigsOrg checklist and the HostAssociated + Extension + title: MigsOrg combined with HostAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HostAssociated + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016002 + MigsOrgHumanAssociated: + name: MigsOrgHumanAssociated + description: MIxS data that complies with the MigsOrg checklist and the HumanAssociated + Extension + title: MigsOrg combined with HumanAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanAssociated + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016003 + MigsOrgHumanGut: + name: MigsOrgHumanGut + description: MIxS data that complies with the MigsOrg checklist and the HumanGut + Extension + title: MigsOrg combined with HumanGut + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanGut + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016004 + MigsOrgHumanOral: + name: MigsOrgHumanOral + description: MIxS data that complies with the MigsOrg checklist and the HumanOral + Extension + title: MigsOrg combined with HumanOral + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanOral + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016005 + MigsOrgHumanSkin: + name: MigsOrgHumanSkin + description: MIxS data that complies with the MigsOrg checklist and the HumanSkin + Extension + title: MigsOrg combined with HumanSkin + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanSkin + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016006 + MigsOrgHumanVaginal: + name: MigsOrgHumanVaginal + description: MIxS data that complies with the MigsOrg checklist and the HumanVaginal + Extension + title: MigsOrg combined with HumanVaginal + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanVaginal + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016007 + MigsOrgHydrocarbonResourcesCores: + name: MigsOrgHydrocarbonResourcesCores + description: MIxS data that complies with the MigsOrg checklist and the HydrocarbonResourcesCores + Extension + title: MigsOrg combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesCores + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016015 + MigsOrgHydrocarbonResourcesFluidsSwabs: + name: MigsOrgHydrocarbonResourcesFluidsSwabs + description: MIxS data that complies with the MigsOrg checklist and the HydrocarbonResourcesFluidsSwabs + Extension + title: MigsOrg combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016016 + MigsOrgMicrobialMatBiofilm: + name: MigsOrgMicrobialMatBiofilm + description: MIxS data that complies with the MigsOrg checklist and the MicrobialMatBiofilm + Extension + title: MigsOrg combined with MicrobialMatBiofilm + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MicrobialMatBiofilm + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016008 + MigsOrgMiscellaneousNaturalOrArtificialEnvironment: + name: MigsOrgMiscellaneousNaturalOrArtificialEnvironment + description: MIxS data that complies with the MigsOrg checklist and the MiscellaneousNaturalOrArtificialEnvironment + Extension + title: MigsOrg combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016009 + MigsOrgPlantAssociated: + name: MigsOrgPlantAssociated + description: MIxS data that complies with the MigsOrg checklist and the PlantAssociated + Extension + title: MigsOrg combined with PlantAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: PlantAssociated + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016010 + MigsOrgSediment: + name: MigsOrgSediment + description: MIxS data that complies with the MigsOrg checklist and the Sediment + Extension + title: MigsOrg combined with Sediment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Sediment + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016011 + MigsOrgSoil: + name: MigsOrgSoil + description: MIxS data that complies with the MigsOrg checklist and the Soil Extension + title: MigsOrg combined with Soil + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Soil + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016012 + MigsOrgSymbiontAssociated: + name: MigsOrgSymbiontAssociated + description: MIxS data that complies with the MigsOrg checklist and the SymbiontAssociated + Extension + title: MigsOrg combined with SymbiontAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: SymbiontAssociated + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016023 + MigsOrgWastewaterSludge: + name: MigsOrgWastewaterSludge + description: MIxS data that complies with the MigsOrg checklist and the WastewaterSludge + Extension + title: MigsOrg combined with WastewaterSludge + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: WastewaterSludge + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016013 + MigsOrgWater: + name: MigsOrgWater + description: MIxS data that complies with the MigsOrg checklist and the Water + Extension + title: MigsOrg combined with Water + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Water + mixins: + - MigsOrg + class_uri: MIXS:0010006_0016014 + MigsPlAgriculture: + name: MigsPlAgriculture + description: MIxS data that complies with the MigsPl checklist and the Agriculture + Extension + title: MigsPl combined with Agriculture + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Agriculture + mixins: + - MigsPl + class_uri: MIXS:0010004_0016018 + MigsPlAir: + name: MigsPlAir + description: MIxS data that complies with the MigsPl checklist and the Air Extension + title: MigsPl combined with Air + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Air + mixins: + - MigsPl + class_uri: MIXS:0010004_0016000 + MigsPlBuiltEnvironment: + name: MigsPlBuiltEnvironment + description: MIxS data that complies with the MigsPl checklist and the BuiltEnvironment + Extension + title: MigsPl combined with BuiltEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: BuiltEnvironment + mixins: + - MigsPl + class_uri: MIXS:0010004_0016001 + MigsPlFoodAnimalAndAnimalFeed: + name: MigsPlFoodAnimalAndAnimalFeed + description: MIxS data that complies with the MigsPl checklist and the FoodAnimalAndAnimalFeed + Extension + title: MigsPl combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodAnimalAndAnimalFeed + mixins: + - MigsPl + class_uri: MIXS:0010004_0016019 + MigsPlFoodFarmEnvironment: + name: MigsPlFoodFarmEnvironment + description: MIxS data that complies with the MigsPl checklist and the FoodFarmEnvironment + Extension + title: MigsPl combined with FoodFarmEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFarmEnvironment + mixins: + - MigsPl + class_uri: MIXS:0010004_0016020 + MigsPlFoodFoodProductionFacility: + name: MigsPlFoodFoodProductionFacility + description: MIxS data that complies with the MigsPl checklist and the FoodFoodProductionFacility + Extension + title: MigsPl combined with FoodFoodProductionFacility + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFoodProductionFacility + mixins: + - MigsPl + class_uri: MIXS:0010004_0016021 + MigsPlFoodHumanFoods: + name: MigsPlFoodHumanFoods + description: MIxS data that complies with the MigsPl checklist and the FoodHumanFoods + Extension + title: MigsPl combined with FoodHumanFoods + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodHumanFoods + mixins: + - MigsPl + class_uri: MIXS:0010004_0016022 + MigsPlHostAssociated: + name: MigsPlHostAssociated + description: MIxS data that complies with the MigsPl checklist and the HostAssociated + Extension + title: MigsPl combined with HostAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HostAssociated + mixins: + - MigsPl + class_uri: MIXS:0010004_0016002 + MigsPlHumanAssociated: + name: MigsPlHumanAssociated + description: MIxS data that complies with the MigsPl checklist and the HumanAssociated + Extension + title: MigsPl combined with HumanAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanAssociated + mixins: + - MigsPl + class_uri: MIXS:0010004_0016003 + MigsPlHumanGut: + name: MigsPlHumanGut + description: MIxS data that complies with the MigsPl checklist and the HumanGut + Extension + title: MigsPl combined with HumanGut + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanGut + mixins: + - MigsPl + class_uri: MIXS:0010004_0016004 + MigsPlHumanOral: + name: MigsPlHumanOral + description: MIxS data that complies with the MigsPl checklist and the HumanOral + Extension + title: MigsPl combined with HumanOral + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanOral + mixins: + - MigsPl + class_uri: MIXS:0010004_0016005 + MigsPlHumanSkin: + name: MigsPlHumanSkin + description: MIxS data that complies with the MigsPl checklist and the HumanSkin + Extension + title: MigsPl combined with HumanSkin + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanSkin + mixins: + - MigsPl + class_uri: MIXS:0010004_0016006 + MigsPlHumanVaginal: + name: MigsPlHumanVaginal + description: MIxS data that complies with the MigsPl checklist and the HumanVaginal + Extension + title: MigsPl combined with HumanVaginal + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanVaginal + mixins: + - MigsPl + class_uri: MIXS:0010004_0016007 + MigsPlHydrocarbonResourcesCores: + name: MigsPlHydrocarbonResourcesCores + description: MIxS data that complies with the MigsPl checklist and the HydrocarbonResourcesCores + Extension + title: MigsPl combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesCores + mixins: + - MigsPl + class_uri: MIXS:0010004_0016015 + MigsPlHydrocarbonResourcesFluidsSwabs: + name: MigsPlHydrocarbonResourcesFluidsSwabs + description: MIxS data that complies with the MigsPl checklist and the HydrocarbonResourcesFluidsSwabs + Extension + title: MigsPl combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - MigsPl + class_uri: MIXS:0010004_0016016 + MigsPlMicrobialMatBiofilm: + name: MigsPlMicrobialMatBiofilm + description: MIxS data that complies with the MigsPl checklist and the MicrobialMatBiofilm + Extension + title: MigsPl combined with MicrobialMatBiofilm + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MicrobialMatBiofilm + mixins: + - MigsPl + class_uri: MIXS:0010004_0016008 + MigsPlMiscellaneousNaturalOrArtificialEnvironment: + name: MigsPlMiscellaneousNaturalOrArtificialEnvironment + description: MIxS data that complies with the MigsPl checklist and the MiscellaneousNaturalOrArtificialEnvironment + Extension + title: MigsPl combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - MigsPl + class_uri: MIXS:0010004_0016009 + MigsPlPlantAssociated: + name: MigsPlPlantAssociated + description: MIxS data that complies with the MigsPl checklist and the PlantAssociated + Extension + title: MigsPl combined with PlantAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: PlantAssociated + mixins: + - MigsPl + class_uri: MIXS:0010004_0016010 + MigsPlSediment: + name: MigsPlSediment + description: MIxS data that complies with the MigsPl checklist and the Sediment + Extension + title: MigsPl combined with Sediment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Sediment + mixins: + - MigsPl + class_uri: MIXS:0010004_0016011 + MigsPlSoil: + name: MigsPlSoil + description: MIxS data that complies with the MigsPl checklist and the Soil Extension + title: MigsPl combined with Soil + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Soil + mixins: + - MigsPl + class_uri: MIXS:0010004_0016012 + MigsPlSymbiontAssociated: + name: MigsPlSymbiontAssociated + description: MIxS data that complies with the MigsPl checklist and the SymbiontAssociated + Extension + title: MigsPl combined with SymbiontAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: SymbiontAssociated + mixins: + - MigsPl + class_uri: MIXS:0010004_0016023 + MigsPlWastewaterSludge: + name: MigsPlWastewaterSludge + description: MIxS data that complies with the MigsPl checklist and the WastewaterSludge + Extension + title: MigsPl combined with WastewaterSludge + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: WastewaterSludge + mixins: + - MigsPl + class_uri: MIXS:0010004_0016013 + MigsPlWater: + name: MigsPlWater + description: MIxS data that complies with the MigsPl checklist and the Water Extension + title: MigsPl combined with Water + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Water + mixins: + - MigsPl + class_uri: MIXS:0010004_0016014 + MigsViAgriculture: + name: MigsViAgriculture + description: MIxS data that complies with the MigsVi checklist and the Agriculture + Extension + title: MigsVi combined with Agriculture + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Agriculture + mixins: + - MigsVi + class_uri: MIXS:0010005_0016018 + MigsViAir: + name: MigsViAir + description: MIxS data that complies with the MigsVi checklist and the Air Extension + title: MigsVi combined with Air + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Air + mixins: + - MigsVi + class_uri: MIXS:0010005_0016000 + MigsViBuiltEnvironment: + name: MigsViBuiltEnvironment + description: MIxS data that complies with the MigsVi checklist and the BuiltEnvironment + Extension + title: MigsVi combined with BuiltEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: BuiltEnvironment + mixins: + - MigsVi + class_uri: MIXS:0010005_0016001 + MigsViFoodAnimalAndAnimalFeed: + name: MigsViFoodAnimalAndAnimalFeed + description: MIxS data that complies with the MigsVi checklist and the FoodAnimalAndAnimalFeed + Extension + title: MigsVi combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodAnimalAndAnimalFeed + mixins: + - MigsVi + class_uri: MIXS:0010005_0016019 + MigsViFoodFarmEnvironment: + name: MigsViFoodFarmEnvironment + description: MIxS data that complies with the MigsVi checklist and the FoodFarmEnvironment + Extension + title: MigsVi combined with FoodFarmEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFarmEnvironment + mixins: + - MigsVi + class_uri: MIXS:0010005_0016020 + MigsViFoodFoodProductionFacility: + name: MigsViFoodFoodProductionFacility + description: MIxS data that complies with the MigsVi checklist and the FoodFoodProductionFacility + Extension + title: MigsVi combined with FoodFoodProductionFacility + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFoodProductionFacility + mixins: + - MigsVi + class_uri: MIXS:0010005_0016021 + MigsViFoodHumanFoods: + name: MigsViFoodHumanFoods + description: MIxS data that complies with the MigsVi checklist and the FoodHumanFoods + Extension + title: MigsVi combined with FoodHumanFoods + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodHumanFoods + mixins: + - MigsVi + class_uri: MIXS:0010005_0016022 + MigsViHostAssociated: + name: MigsViHostAssociated + description: MIxS data that complies with the MigsVi checklist and the HostAssociated + Extension + title: MigsVi combined with HostAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HostAssociated + mixins: + - MigsVi + class_uri: MIXS:0010005_0016002 + MigsViHumanAssociated: + name: MigsViHumanAssociated + description: MIxS data that complies with the MigsVi checklist and the HumanAssociated + Extension + title: MigsVi combined with HumanAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanAssociated + mixins: + - MigsVi + class_uri: MIXS:0010005_0016003 + MigsViHumanGut: + name: MigsViHumanGut + description: MIxS data that complies with the MigsVi checklist and the HumanGut + Extension + title: MigsVi combined with HumanGut + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanGut + mixins: + - MigsVi + class_uri: MIXS:0010005_0016004 + MigsViHumanOral: + name: MigsViHumanOral + description: MIxS data that complies with the MigsVi checklist and the HumanOral + Extension + title: MigsVi combined with HumanOral + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanOral + mixins: + - MigsVi + class_uri: MIXS:0010005_0016005 + MigsViHumanSkin: + name: MigsViHumanSkin + description: MIxS data that complies with the MigsVi checklist and the HumanSkin + Extension + title: MigsVi combined with HumanSkin + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanSkin + mixins: + - MigsVi + class_uri: MIXS:0010005_0016006 + MigsViHumanVaginal: + name: MigsViHumanVaginal + description: MIxS data that complies with the MigsVi checklist and the HumanVaginal + Extension + title: MigsVi combined with HumanVaginal + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanVaginal + mixins: + - MigsVi + class_uri: MIXS:0010005_0016007 + MigsViHydrocarbonResourcesCores: + name: MigsViHydrocarbonResourcesCores + description: MIxS data that complies with the MigsVi checklist and the HydrocarbonResourcesCores + Extension + title: MigsVi combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesCores + mixins: + - MigsVi + class_uri: MIXS:0010005_0016015 + MigsViHydrocarbonResourcesFluidsSwabs: + name: MigsViHydrocarbonResourcesFluidsSwabs + description: MIxS data that complies with the MigsVi checklist and the HydrocarbonResourcesFluidsSwabs + Extension + title: MigsVi combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - MigsVi + class_uri: MIXS:0010005_0016016 + MigsViMicrobialMatBiofilm: + name: MigsViMicrobialMatBiofilm + description: MIxS data that complies with the MigsVi checklist and the MicrobialMatBiofilm + Extension + title: MigsVi combined with MicrobialMatBiofilm + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MicrobialMatBiofilm + mixins: + - MigsVi + class_uri: MIXS:0010005_0016008 + MigsViMiscellaneousNaturalOrArtificialEnvironment: + name: MigsViMiscellaneousNaturalOrArtificialEnvironment + description: MIxS data that complies with the MigsVi checklist and the MiscellaneousNaturalOrArtificialEnvironment + Extension + title: MigsVi combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - MigsVi + class_uri: MIXS:0010005_0016009 + MigsViPlantAssociated: + name: MigsViPlantAssociated + description: MIxS data that complies with the MigsVi checklist and the PlantAssociated + Extension + title: MigsVi combined with PlantAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: PlantAssociated + mixins: + - MigsVi + class_uri: MIXS:0010005_0016010 + MigsViSediment: + name: MigsViSediment + description: MIxS data that complies with the MigsVi checklist and the Sediment + Extension + title: MigsVi combined with Sediment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Sediment + mixins: + - MigsVi + class_uri: MIXS:0010005_0016011 + MigsViSoil: + name: MigsViSoil + description: MIxS data that complies with the MigsVi checklist and the Soil Extension + title: MigsVi combined with Soil + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Soil + mixins: + - MigsVi + class_uri: MIXS:0010005_0016012 + MigsViSymbiontAssociated: + name: MigsViSymbiontAssociated + description: MIxS data that complies with the MigsVi checklist and the SymbiontAssociated + Extension + title: MigsVi combined with SymbiontAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: SymbiontAssociated + mixins: + - MigsVi + class_uri: MIXS:0010005_0016023 + MigsViWastewaterSludge: + name: MigsViWastewaterSludge + description: MIxS data that complies with the MigsVi checklist and the WastewaterSludge + Extension + title: MigsVi combined with WastewaterSludge + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: WastewaterSludge + mixins: + - MigsVi + class_uri: MIXS:0010005_0016013 + MigsViWater: + name: MigsViWater + description: MIxS data that complies with the MigsVi checklist and the Water Extension + title: MigsVi combined with Water + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Water + mixins: + - MigsVi + class_uri: MIXS:0010005_0016014 + MimagAgriculture: + name: MimagAgriculture + description: MIxS data that complies with the Mimag checklist and the Agriculture + Extension + title: Mimag combined with Agriculture + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Agriculture + mixins: + - Mimag + class_uri: MIXS:0010011_0016018 + MimagAir: + name: MimagAir + description: MIxS data that complies with the Mimag checklist and the Air Extension + title: Mimag combined with Air + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Air + mixins: + - Mimag + class_uri: MIXS:0010011_0016000 + MimagBuiltEnvironment: + name: MimagBuiltEnvironment + description: MIxS data that complies with the Mimag checklist and the BuiltEnvironment + Extension + title: Mimag combined with BuiltEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: BuiltEnvironment + mixins: + - Mimag + class_uri: MIXS:0010011_0016001 + MimagFoodAnimalAndAnimalFeed: + name: MimagFoodAnimalAndAnimalFeed + description: MIxS data that complies with the Mimag checklist and the FoodAnimalAndAnimalFeed + Extension + title: Mimag combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodAnimalAndAnimalFeed + mixins: + - Mimag + class_uri: MIXS:0010011_0016019 + MimagFoodFarmEnvironment: + name: MimagFoodFarmEnvironment + description: MIxS data that complies with the Mimag checklist and the FoodFarmEnvironment + Extension + title: Mimag combined with FoodFarmEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFarmEnvironment + mixins: + - Mimag + class_uri: MIXS:0010011_0016020 + MimagFoodFoodProductionFacility: + name: MimagFoodFoodProductionFacility + description: MIxS data that complies with the Mimag checklist and the FoodFoodProductionFacility + Extension + title: Mimag combined with FoodFoodProductionFacility + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFoodProductionFacility + mixins: + - Mimag + class_uri: MIXS:0010011_0016021 + MimagFoodHumanFoods: + name: MimagFoodHumanFoods + description: MIxS data that complies with the Mimag checklist and the FoodHumanFoods + Extension + title: Mimag combined with FoodHumanFoods + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodHumanFoods + mixins: + - Mimag + class_uri: MIXS:0010011_0016022 + MimagHostAssociated: + name: MimagHostAssociated + description: MIxS data that complies with the Mimag checklist and the HostAssociated + Extension + title: Mimag combined with HostAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HostAssociated + mixins: + - Mimag + class_uri: MIXS:0010011_0016002 + MimagHumanAssociated: + name: MimagHumanAssociated + description: MIxS data that complies with the Mimag checklist and the HumanAssociated + Extension + title: Mimag combined with HumanAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanAssociated + mixins: + - Mimag + class_uri: MIXS:0010011_0016003 + MimagHumanGut: + name: MimagHumanGut + description: MIxS data that complies with the Mimag checklist and the HumanGut + Extension + title: Mimag combined with HumanGut + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanGut + mixins: + - Mimag + class_uri: MIXS:0010011_0016004 + MimagHumanOral: + name: MimagHumanOral + description: MIxS data that complies with the Mimag checklist and the HumanOral + Extension + title: Mimag combined with HumanOral + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanOral + mixins: + - Mimag + class_uri: MIXS:0010011_0016005 + MimagHumanSkin: + name: MimagHumanSkin + description: MIxS data that complies with the Mimag checklist and the HumanSkin + Extension + title: Mimag combined with HumanSkin + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanSkin + mixins: + - Mimag + class_uri: MIXS:0010011_0016006 + MimagHumanVaginal: + name: MimagHumanVaginal + description: MIxS data that complies with the Mimag checklist and the HumanVaginal + Extension + title: Mimag combined with HumanVaginal + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanVaginal + mixins: + - Mimag + class_uri: MIXS:0010011_0016007 + MimagHydrocarbonResourcesCores: + name: MimagHydrocarbonResourcesCores + description: MIxS data that complies with the Mimag checklist and the HydrocarbonResourcesCores + Extension + title: Mimag combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesCores + mixins: + - Mimag + class_uri: MIXS:0010011_0016015 + MimagHydrocarbonResourcesFluidsSwabs: + name: MimagHydrocarbonResourcesFluidsSwabs + description: MIxS data that complies with the Mimag checklist and the HydrocarbonResourcesFluidsSwabs + Extension + title: Mimag combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - Mimag + class_uri: MIXS:0010011_0016016 + MimagMicrobialMatBiofilm: + name: MimagMicrobialMatBiofilm + description: MIxS data that complies with the Mimag checklist and the MicrobialMatBiofilm + Extension + title: Mimag combined with MicrobialMatBiofilm + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MicrobialMatBiofilm + mixins: + - Mimag + class_uri: MIXS:0010011_0016008 + MimagMiscellaneousNaturalOrArtificialEnvironment: + name: MimagMiscellaneousNaturalOrArtificialEnvironment + description: MIxS data that complies with the Mimag checklist and the MiscellaneousNaturalOrArtificialEnvironment + Extension + title: Mimag combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - Mimag + class_uri: MIXS:0010011_0016009 + MimagPlantAssociated: + name: MimagPlantAssociated + description: MIxS data that complies with the Mimag checklist and the PlantAssociated + Extension + title: Mimag combined with PlantAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: PlantAssociated + mixins: + - Mimag + class_uri: MIXS:0010011_0016010 + MimagSediment: + name: MimagSediment + description: MIxS data that complies with the Mimag checklist and the Sediment + Extension + title: Mimag combined with Sediment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Sediment + mixins: + - Mimag + class_uri: MIXS:0010011_0016011 + MimagSoil: + name: MimagSoil + description: MIxS data that complies with the Mimag checklist and the Soil Extension + title: Mimag combined with Soil + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Soil + mixins: + - Mimag + class_uri: MIXS:0010011_0016012 + MimagSymbiontAssociated: + name: MimagSymbiontAssociated + description: MIxS data that complies with the Mimag checklist and the SymbiontAssociated + Extension + title: Mimag combined with SymbiontAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: SymbiontAssociated + mixins: + - Mimag + class_uri: MIXS:0010011_0016023 + MimagWastewaterSludge: + name: MimagWastewaterSludge + description: MIxS data that complies with the Mimag checklist and the WastewaterSludge + Extension + title: Mimag combined with WastewaterSludge + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: WastewaterSludge + mixins: + - Mimag + class_uri: MIXS:0010011_0016013 + MimagWater: + name: MimagWater + description: MIxS data that complies with the Mimag checklist and the Water Extension + title: Mimag combined with Water + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Water + mixins: + - Mimag + class_uri: MIXS:0010011_0016014 + MimarksCAgriculture: + name: MimarksCAgriculture + description: MIxS data that complies with the MimarksC checklist and the Agriculture + Extension + title: MimarksC combined with Agriculture + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Agriculture + mixins: + - MimarksC + class_uri: MIXS:0010009_0016018 + MimarksCAir: + name: MimarksCAir + description: MIxS data that complies with the MimarksC checklist and the Air Extension + title: MimarksC combined with Air + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Air + mixins: + - MimarksC + class_uri: MIXS:0010009_0016000 + MimarksCBuiltEnvironment: + name: MimarksCBuiltEnvironment + description: MIxS data that complies with the MimarksC checklist and the BuiltEnvironment + Extension + title: MimarksC combined with BuiltEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: BuiltEnvironment + mixins: + - MimarksC + class_uri: MIXS:0010009_0016001 + MimarksCFoodAnimalAndAnimalFeed: + name: MimarksCFoodAnimalAndAnimalFeed + description: MIxS data that complies with the MimarksC checklist and the FoodAnimalAndAnimalFeed + Extension + title: MimarksC combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodAnimalAndAnimalFeed + mixins: + - MimarksC + class_uri: MIXS:0010009_0016019 + MimarksCFoodFarmEnvironment: + name: MimarksCFoodFarmEnvironment + description: MIxS data that complies with the MimarksC checklist and the FoodFarmEnvironment + Extension + title: MimarksC combined with FoodFarmEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFarmEnvironment + mixins: + - MimarksC + class_uri: MIXS:0010009_0016020 + MimarksCFoodFoodProductionFacility: + name: MimarksCFoodFoodProductionFacility + description: MIxS data that complies with the MimarksC checklist and the FoodFoodProductionFacility + Extension + title: MimarksC combined with FoodFoodProductionFacility + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFoodProductionFacility + mixins: + - MimarksC + class_uri: MIXS:0010009_0016021 + MimarksCFoodHumanFoods: + name: MimarksCFoodHumanFoods + description: MIxS data that complies with the MimarksC checklist and the FoodHumanFoods + Extension + title: MimarksC combined with FoodHumanFoods + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodHumanFoods + mixins: + - MimarksC + class_uri: MIXS:0010009_0016022 + MimarksCHostAssociated: + name: MimarksCHostAssociated + description: MIxS data that complies with the MimarksC checklist and the HostAssociated + Extension + title: MimarksC combined with HostAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HostAssociated + mixins: + - MimarksC + class_uri: MIXS:0010009_0016002 + MimarksCHumanAssociated: + name: MimarksCHumanAssociated + description: MIxS data that complies with the MimarksC checklist and the HumanAssociated + Extension + title: MimarksC combined with HumanAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanAssociated + mixins: + - MimarksC + class_uri: MIXS:0010009_0016003 + MimarksCHumanGut: + name: MimarksCHumanGut + description: MIxS data that complies with the MimarksC checklist and the HumanGut + Extension + title: MimarksC combined with HumanGut + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanGut + mixins: + - MimarksC + class_uri: MIXS:0010009_0016004 + MimarksCHumanOral: + name: MimarksCHumanOral + description: MIxS data that complies with the MimarksC checklist and the HumanOral + Extension + title: MimarksC combined with HumanOral + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanOral + mixins: + - MimarksC + class_uri: MIXS:0010009_0016005 + MimarksCHumanSkin: + name: MimarksCHumanSkin + description: MIxS data that complies with the MimarksC checklist and the HumanSkin + Extension + title: MimarksC combined with HumanSkin + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanSkin + mixins: + - MimarksC + class_uri: MIXS:0010009_0016006 + MimarksCHumanVaginal: + name: MimarksCHumanVaginal + description: MIxS data that complies with the MimarksC checklist and the HumanVaginal + Extension + title: MimarksC combined with HumanVaginal + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanVaginal + mixins: + - MimarksC + class_uri: MIXS:0010009_0016007 + MimarksCHydrocarbonResourcesCores: + name: MimarksCHydrocarbonResourcesCores + description: MIxS data that complies with the MimarksC checklist and the HydrocarbonResourcesCores + Extension + title: MimarksC combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesCores + mixins: + - MimarksC + class_uri: MIXS:0010009_0016015 + MimarksCHydrocarbonResourcesFluidsSwabs: + name: MimarksCHydrocarbonResourcesFluidsSwabs + description: MIxS data that complies with the MimarksC checklist and the HydrocarbonResourcesFluidsSwabs + Extension + title: MimarksC combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - MimarksC + class_uri: MIXS:0010009_0016016 + MimarksCMicrobialMatBiofilm: + name: MimarksCMicrobialMatBiofilm + description: MIxS data that complies with the MimarksC checklist and the MicrobialMatBiofilm + Extension + title: MimarksC combined with MicrobialMatBiofilm + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MicrobialMatBiofilm + mixins: + - MimarksC + class_uri: MIXS:0010009_0016008 + MimarksCMiscellaneousNaturalOrArtificialEnvironment: + name: MimarksCMiscellaneousNaturalOrArtificialEnvironment + description: MIxS data that complies with the MimarksC checklist and the MiscellaneousNaturalOrArtificialEnvironment + Extension + title: MimarksC combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - MimarksC + class_uri: MIXS:0010009_0016009 + MimarksCPlantAssociated: + name: MimarksCPlantAssociated + description: MIxS data that complies with the MimarksC checklist and the PlantAssociated + Extension + title: MimarksC combined with PlantAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: PlantAssociated + mixins: + - MimarksC + class_uri: MIXS:0010009_0016010 + MimarksCSediment: + name: MimarksCSediment + description: MIxS data that complies with the MimarksC checklist and the Sediment + Extension + title: MimarksC combined with Sediment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Sediment + mixins: + - MimarksC + class_uri: MIXS:0010009_0016011 + MimarksCSoil: + name: MimarksCSoil + description: MIxS data that complies with the MimarksC checklist and the Soil + Extension + title: MimarksC combined with Soil + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Soil + mixins: + - MimarksC + class_uri: MIXS:0010009_0016012 + MimarksCSymbiontAssociated: + name: MimarksCSymbiontAssociated + description: MIxS data that complies with the MimarksC checklist and the SymbiontAssociated + Extension + title: MimarksC combined with SymbiontAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: SymbiontAssociated + mixins: + - MimarksC + class_uri: MIXS:0010009_0016023 + MimarksCWastewaterSludge: + name: MimarksCWastewaterSludge + description: MIxS data that complies with the MimarksC checklist and the WastewaterSludge + Extension + title: MimarksC combined with WastewaterSludge + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: WastewaterSludge + mixins: + - MimarksC + class_uri: MIXS:0010009_0016013 + MimarksCWater: + name: MimarksCWater + description: MIxS data that complies with the MimarksC checklist and the Water + Extension + title: MimarksC combined with Water + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Water + mixins: + - MimarksC + class_uri: MIXS:0010009_0016014 + MimarksSAgriculture: + name: MimarksSAgriculture + description: MIxS data that complies with the MimarksS checklist and the Agriculture + Extension + title: MimarksS combined with Agriculture + in_subset: + - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - is_a: Extension - slots: - - samp_name - - project_name - - depth - - elev - - alkalinity - - alkyl_diethers - - aminopept_act - - ammonium - - bacteria_carb_prod - - biomass - - bishomohopanol - - bromide - - calcium - - carb_nitro_ratio - - chem_administration - - chloride - - chlorophyll - - density - - diether_lipids - - diss_carb_dioxide - - diss_hydrogen - - diss_inorg_carb - - diss_org_carb - - diss_org_nitro - - diss_oxygen - - glucosidase_act - - magnesium - - mean_frict_vel - - mean_peak_frict_vel - - methane - - misc_param - - n_alkanes - - nitrate - - nitrite - - nitro - - org_carb - - org_matter - - org_nitro - - organism_count - - oxy_stat_samp - - ph - - particle_class - - part_org_carb - - perturbation - - petroleum_hydrocarb - - phaeopigments - - phosphate - - phosplipid_fatt_acid - - porosity - - potassium - - pressure - - redox_potential - - salinity - - samp_store_dur - - samp_store_loc - - samp_store_temp - - samp_vol_we_dna_ext - - sediment_type - - silicate - - sodium - - sulfate - - sulfide - - temp - - tidal_stage - - tot_carb - - tot_depth_water_col - - tot_nitro_content - - tot_org_carb - - turbidity - - water_content - slot_usage: - alkyl_diethers: - name: alkyl_diethers - ammonium: - name: ammonium - required: false - recommended: false - bacteria_carb_prod: - name: bacteria_carb_prod - chem_administration: - name: chem_administration - required: false - recommended: false - depth: - name: depth - examples: - - value: 10 meter - required: true - diss_org_nitro: - name: diss_org_nitro - elev: - name: elev - recommended: true - methane: - name: methane - examples: - - value: 0.15 micromole per liter - n_alkanes: - name: n_alkanes - nitrate: - name: nitrate - required: false - recommended: false - nitrite: - name: nitrite - required: false - recommended: false - org_carb: - name: org_carb - org_nitro: - name: org_nitro - organism_count: - name: organism_count - examples: - - value: total prokaryotes;3.5e7 cells per milliliter;qPCR - required: false - recommended: false - oxy_stat_samp: - name: oxy_stat_samp - required: false - recommended: false - part_org_carb: - name: part_org_carb - perturbation: - name: perturbation - required: false - recommended: false - ph: - name: ph - required: false - recommended: false - phosplipid_fatt_acid: - name: phosplipid_fatt_acid - samp_store_dur: - name: samp_store_dur - required: false - recommended: false - samp_store_loc: - name: samp_store_loc - required: false - recommended: false - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - sulfate: - name: sulfate - required: false - recommended: false - sulfide: - name: sulfide - required: false - recommended: false - temp: - name: temp - required: false - recommended: false - tot_carb: - name: tot_carb - required: false - recommended: false - tot_nitro_content: - name: tot_nitro_content - required: false - recommended: false - tot_org_carb: - name: tot_org_carb - required: false - recommended: false - turbidity: - name: turbidity - water_content: - name: water_content - string_serialization: '{float} {unit}' - class_uri: MIXS:0016011 - Soil: - name: Soil - description: soil extension - title: soil + is_a: Agriculture + mixins: + - MimarksS + class_uri: MIXS:0010008_0016018 + MimarksSAir: + name: MimarksSAir + description: MIxS data that complies with the MimarksS checklist and the Air Extension + title: MimarksS combined with Air + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Air + mixins: + - MimarksS + class_uri: MIXS:0010008_0016000 + MimarksSBuiltEnvironment: + name: MimarksSBuiltEnvironment + description: MIxS data that complies with the MimarksS checklist and the BuiltEnvironment + Extension + title: MimarksS combined with BuiltEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: BuiltEnvironment + mixins: + - MimarksS + class_uri: MIXS:0010008_0016001 + MimarksSFoodAnimalAndAnimalFeed: + name: MimarksSFoodAnimalAndAnimalFeed + description: MIxS data that complies with the MimarksS checklist and the FoodAnimalAndAnimalFeed + Extension + title: MimarksS combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodAnimalAndAnimalFeed + mixins: + - MimarksS + class_uri: MIXS:0010008_0016019 + MimarksSFoodFarmEnvironment: + name: MimarksSFoodFarmEnvironment + description: MIxS data that complies with the MimarksS checklist and the FoodFarmEnvironment + Extension + title: MimarksS combined with FoodFarmEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFarmEnvironment + mixins: + - MimarksS + class_uri: MIXS:0010008_0016020 + MimarksSFoodFoodProductionFacility: + name: MimarksSFoodFoodProductionFacility + description: MIxS data that complies with the MimarksS checklist and the FoodFoodProductionFacility + Extension + title: MimarksS combined with FoodFoodProductionFacility + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFoodProductionFacility + mixins: + - MimarksS + class_uri: MIXS:0010008_0016021 + MimarksSFoodHumanFoods: + name: MimarksSFoodHumanFoods + description: MIxS data that complies with the MimarksS checklist and the FoodHumanFoods + Extension + title: MimarksS combined with FoodHumanFoods + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodHumanFoods + mixins: + - MimarksS + class_uri: MIXS:0010008_0016022 + MimarksSHostAssociated: + name: MimarksSHostAssociated + description: MIxS data that complies with the MimarksS checklist and the HostAssociated + Extension + title: MimarksS combined with HostAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HostAssociated + mixins: + - MimarksS + class_uri: MIXS:0010008_0016002 + MimarksSHumanAssociated: + name: MimarksSHumanAssociated + description: MIxS data that complies with the MimarksS checklist and the HumanAssociated + Extension + title: MimarksS combined with HumanAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanAssociated + mixins: + - MimarksS + class_uri: MIXS:0010008_0016003 + MimarksSHumanGut: + name: MimarksSHumanGut + description: MIxS data that complies with the MimarksS checklist and the HumanGut + Extension + title: MimarksS combined with HumanGut + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanGut + mixins: + - MimarksS + class_uri: MIXS:0010008_0016004 + MimarksSHumanOral: + name: MimarksSHumanOral + description: MIxS data that complies with the MimarksS checklist and the HumanOral + Extension + title: MimarksS combined with HumanOral + in_subset: + - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - is_a: Extension - slots: - - samp_name - - project_name - - depth - - elev - - cur_land_use - - cur_vegetation - - cur_vegetation_meth - - previous_land_use - - prev_land_use_meth - - crop_rotation - - agrochem_addition - - tillage - - fire - - flooding - - extreme_event - - soil_horizon - - horizon_meth - - sieving - - water_content - - water_cont_soil_meth - - samp_vol_we_dna_ext - - pool_dna_extracts - - store_cond - - link_climate_info - - annual_temp - - season_temp - - annual_precpt - - season_precpt - - link_class_info - - fao_class - - local_class - - local_class_meth - - org_nitro - - temp - - soil_type - - soil_type_meth - - slope_gradient - - slope_aspect - - profile_position - - drainage_class - - soil_texture - - soil_texture_meth - - ph - - ph_meth - - org_matter - - tot_org_carb - - tot_org_c_meth - - tot_nitro_content - - tot_nitro_cont_meth - - microbial_biomass - - micro_biomass_meth - - link_addit_analys - - heavy_metals - - heavy_metals_meth - - al_sat - - al_sat_meth - - misc_param - slot_usage: - crop_rotation: - name: crop_rotation - string_serialization: '{boolean};{Rn/start_time/end_time/duration}' - required: false - recommended: false - cur_vegetation: - name: cur_vegetation - required: false - recommended: false - cur_vegetation_meth: - name: cur_vegetation_meth - required: false - recommended: false - depth: - name: depth - examples: - - value: 10 meter - required: true - drainage_class: - name: drainage_class - required: false - recommended: false - elev: - name: elev - required: true - extreme_event: - name: extreme_event - required: false - recommended: false - fao_class: - name: fao_class - required: false - recommended: false - fire: - name: fire - required: false - recommended: false - flooding: - name: flooding - required: false - recommended: false - heavy_metals_meth: - name: heavy_metals_meth - string_serialization: '{PMID}|{DOI}|{URL}' - required: false - recommended: false - horizon_meth: - name: horizon_meth - required: false - recommended: false - local_class: - name: local_class - required: false - recommended: false - local_class_meth: - name: local_class_meth - required: false - recommended: false - micro_biomass_meth: - name: micro_biomass_meth - required: false - recommended: false - microbial_biomass: - name: microbial_biomass - required: false - recommended: false - org_nitro: - name: org_nitro - ph: - name: ph - required: false - recommended: false - ph_meth: - name: ph_meth - required: false - recommended: false - pool_dna_extracts: - name: pool_dna_extracts - string_serialization: '{boolean};{integer}' - required: false - recommended: false - prev_land_use_meth: - name: prev_land_use_meth - required: false - recommended: false - previous_land_use: - name: previous_land_use - required: false - recommended: false - profile_position: - name: profile_position - required: false - recommended: false - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - season_precpt: - name: season_precpt - sieving: - name: sieving - required: false - recommended: false - slope_aspect: - name: slope_aspect - required: false - recommended: false - slope_gradient: - name: slope_gradient - required: false - recommended: false - soil_horizon: - name: soil_horizon - required: false - recommended: false - soil_type: - name: soil_type - string_serialization: '{termLabel} [{termID}] - - ' - required: false - recommended: false - soil_type_meth: - name: soil_type_meth - required: false - recommended: false - store_cond: - name: store_cond - required: false - recommended: false - temp: - name: temp - required: false - recommended: false - tillage: - name: tillage - required: false - recommended: false - tot_nitro_cont_meth: - name: tot_nitro_cont_meth - required: false - recommended: false - tot_nitro_content: - name: tot_nitro_content - required: false - recommended: false - tot_org_c_meth: - name: tot_org_c_meth - required: false - recommended: false - tot_org_carb: - name: tot_org_carb - required: false - recommended: false - water_content: - name: water_content - string_serialization: '{float}' - class_uri: MIXS:0016012 - SymbiontAssociated: - name: SymbiontAssociated - description: symbiont-associated extension - title: symbiont-associated + is_a: HumanOral + mixins: + - MimarksS + class_uri: MIXS:0010008_0016005 + MimarksSHumanSkin: + name: MimarksSHumanSkin + description: MIxS data that complies with the MimarksS checklist and the HumanSkin + Extension + title: MimarksS combined with HumanSkin + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanSkin + mixins: + - MimarksS + class_uri: MIXS:0010008_0016006 + MimarksSHumanVaginal: + name: MimarksSHumanVaginal + description: MIxS data that complies with the MimarksS checklist and the HumanVaginal + Extension + title: MimarksS combined with HumanVaginal + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanVaginal + mixins: + - MimarksS + class_uri: MIXS:0010008_0016007 + MimarksSHydrocarbonResourcesCores: + name: MimarksSHydrocarbonResourcesCores + description: MIxS data that complies with the MimarksS checklist and the HydrocarbonResourcesCores + Extension + title: MimarksS combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesCores + mixins: + - MimarksS + class_uri: MIXS:0010008_0016015 + MimarksSHydrocarbonResourcesFluidsSwabs: + name: MimarksSHydrocarbonResourcesFluidsSwabs + description: MIxS data that complies with the MimarksS checklist and the HydrocarbonResourcesFluidsSwabs + Extension + title: MimarksS combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - is_a: Extension - slots: - - samp_name - - project_name - - lat_lon - - geo_loc_name - - collection_date - - alt - - depth - - elev - - host_subject_id - - host_common_name - - host_taxid - - source_mat_id - - host_dependence - - type_of_symbiosis - - sym_life_cycle_type - - host_life_stage - - host_age - - urobiom_sex - - mode_transmission - - route_transmission - - host_body_habitat - - host_body_site - - host_body_product - - host_tot_mass - - host_height - - host_length - - host_growth_cond - - host_substrate - - host_fam_rel - - host_infra_spec_name - - host_infra_spec_rank - - host_genotype - - host_phenotype - - host_dry_mass - - host_color - - host_shape - - gravidity - - host_number - - host_symbiont - - host_specificity - - symbiont_host_role - - host_cellular_loc - - association_duration - - host_of_host_coinf - - host_of_host_name - - host_of_host_env_loc - - host_of_host_env_med - - host_of_host_taxid - - host_of_host_sub_id - - host_of_host_disease - - host_of_host_fam_rel - - host_of_host_infname - - host_of_host_infrank - - host_of_host_geno - - host_of_host_pheno - - host_of_host_gravid - - host_of_host_totmass - - chem_administration - - perturbation - - salinity - - oxy_stat_samp - - temp - - organism_count - - samp_vol_we_dna_ext - - samp_store_temp - - samp_store_dur - - samp_store_loc - - samp_store_sol - - misc_param - slot_usage: - alt: - name: alt - recommended: true - chem_administration: - name: chem_administration - required: false - recommended: false - depth: - name: depth - examples: - - value: 10 meter - recommended: true - elev: - name: elev - recommended: true - gravidity: - name: gravidity - host_age: - name: host_age - required: false - recommended: false - host_body_habitat: - name: host_body_habitat - examples: - - value: anterior end of a tapeworm - host_body_site: - name: host_body_site - examples: - - value: scolex [UBERON:0015119] - host_color: - name: host_color - host_common_name: - name: host_common_name - examples: - - value: trematode - required: false - recommended: false - host_fam_rel: - name: host_fam_rel - examples: - - value: clone;P15 - host_genotype: - name: host_genotype - required: false - recommended: false - host_growth_cond: - name: host_growth_cond - host_height: - name: host_height - required: false - recommended: false - host_length: - name: host_length - required: false - recommended: false - host_life_stage: - name: host_life_stage - examples: - - value: redia - required: true - host_phenotype: - name: host_phenotype - examples: - - value: soldier - required: false - recommended: false - host_shape: - name: host_shape - host_subject_id: - name: host_subject_id - examples: - - value: P14 - host_substrate: - name: host_substrate - host_symbiont: - name: host_symbiont - examples: - - value: Paragordius varius - host_taxid: - name: host_taxid - examples: - - value: '395013' - string_serialization: '{integer}' - required: false - recommended: false - host_tot_mass: - name: host_tot_mass - required: false - recommended: false - organism_count: - name: organism_count - examples: - - value: total prokaryotes;3.5e7 cells per milliliter;qPCR - required: false - recommended: false - oxy_stat_samp: - name: oxy_stat_samp - required: false - recommended: false - perturbation: - name: perturbation - required: false - recommended: false - samp_store_dur: - name: samp_store_dur - required: false - recommended: false - samp_store_loc: - name: samp_store_loc - required: false - recommended: false - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - source_mat_id: - name: source_mat_id - required: false - recommended: false - temp: - name: temp - required: false - recommended: false - class_uri: MIXS:0016023 - WastewaterSludge: - name: WastewaterSludge - description: wastewater/sludge extension - title: wastewater/sludge + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - MimarksS + class_uri: MIXS:0010008_0016016 + MimarksSMicrobialMatBiofilm: + name: MimarksSMicrobialMatBiofilm + description: MIxS data that complies with the MimarksS checklist and the MicrobialMatBiofilm + Extension + title: MimarksS combined with MicrobialMatBiofilm + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MicrobialMatBiofilm + mixins: + - MimarksS + class_uri: MIXS:0010008_0016008 + MimarksSMiscellaneousNaturalOrArtificialEnvironment: + name: MimarksSMiscellaneousNaturalOrArtificialEnvironment + description: MIxS data that complies with the MimarksS checklist and the MiscellaneousNaturalOrArtificialEnvironment + Extension + title: MimarksS combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - MimarksS + class_uri: MIXS:0010008_0016009 + MimarksSPlantAssociated: + name: MimarksSPlantAssociated + description: MIxS data that complies with the MimarksS checklist and the PlantAssociated + Extension + title: MimarksS combined with PlantAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: PlantAssociated + mixins: + - MimarksS + class_uri: MIXS:0010008_0016010 + MimarksSSediment: + name: MimarksSSediment + description: MIxS data that complies with the MimarksS checklist and the Sediment + Extension + title: MimarksS combined with Sediment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Sediment + mixins: + - MimarksS + class_uri: MIXS:0010008_0016011 + MimarksSSoil: + name: MimarksSSoil + description: MIxS data that complies with the MimarksS checklist and the Soil + Extension + title: MimarksS combined with Soil + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Soil + mixins: + - MimarksS + class_uri: MIXS:0010008_0016012 + MimarksSSymbiontAssociated: + name: MimarksSSymbiontAssociated + description: MIxS data that complies with the MimarksS checklist and the SymbiontAssociated + Extension + title: MimarksS combined with SymbiontAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: SymbiontAssociated + mixins: + - MimarksS + class_uri: MIXS:0010008_0016023 + MimarksSWastewaterSludge: + name: MimarksSWastewaterSludge + description: MIxS data that complies with the MimarksS checklist and the WastewaterSludge + Extension + title: MimarksS combined with WastewaterSludge + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: WastewaterSludge + mixins: + - MimarksS + class_uri: MIXS:0010008_0016013 + MimarksSWater: + name: MimarksSWater + description: MIxS data that complies with the MimarksS checklist and the Water + Extension + title: MimarksS combined with Water + in_subset: + - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - is_a: Extension - slots: - - samp_name - - project_name - - depth - - alkalinity - - biochem_oxygen_dem - - chem_administration - - chem_oxygen_dem - - efficiency_percent - - emulsions - - gaseous_substances - - indust_eff_percent - - inorg_particles - - misc_param - - nitrate - - org_particles - - organism_count - - oxy_stat_samp - - ph - - perturbation - - phosphate - - pre_treatment - - primary_treatment - - reactor_type - - salinity - - samp_store_dur - - samp_store_loc - - samp_store_temp - - samp_vol_we_dna_ext - - secondary_treatment - - sewage_type - - sludge_retent_time - - sodium - - soluble_inorg_mat - - soluble_org_mat - - suspend_solids - - temp - - tertiary_treatment - - tot_nitro - - tot_phosphate - - wastewater_type - slot_usage: - chem_administration: - name: chem_administration - required: false - recommended: false - depth: - name: depth - examples: - - value: 10 meter - recommended: true - nitrate: - name: nitrate - required: false - recommended: false - organism_count: - name: organism_count - examples: - - value: total prokaryotes;3.5e7 cells per milliliter;qPCR - required: false - recommended: false - oxy_stat_samp: - name: oxy_stat_samp - required: false - recommended: false - perturbation: - name: perturbation - required: false - recommended: false - ph: - name: ph - required: false - recommended: false - samp_store_dur: - name: samp_store_dur - required: false - recommended: false - samp_store_loc: - name: samp_store_loc - required: false - recommended: false - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - temp: - name: temp - required: false - recommended: false - tot_phosphate: - name: tot_phosphate - required: false - recommended: false - class_uri: MIXS:0016013 - Water: - name: Water - description: water extension - title: water + is_a: Water + mixins: + - MimarksS + class_uri: MIXS:0010008_0016014 + MimsAgriculture: + name: MimsAgriculture + description: MIxS data that complies with the Mims checklist and the Agriculture + Extension + title: Mims combined with Agriculture + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Agriculture + mixins: + - Mims + class_uri: MIXS:0010007_0016018 + MimsAir: + name: MimsAir + description: MIxS data that complies with the Mims checklist and the Air Extension + title: Mims combined with Air + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Air + mixins: + - Mims + class_uri: MIXS:0010007_0016000 + MimsBuiltEnvironment: + name: MimsBuiltEnvironment + description: MIxS data that complies with the Mims checklist and the BuiltEnvironment + Extension + title: Mims combined with BuiltEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: BuiltEnvironment + mixins: + - Mims + class_uri: MIXS:0010007_0016001 + MimsFoodAnimalAndAnimalFeed: + name: MimsFoodAnimalAndAnimalFeed + description: MIxS data that complies with the Mims checklist and the FoodAnimalAndAnimalFeed + Extension + title: Mims combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodAnimalAndAnimalFeed + mixins: + - Mims + class_uri: MIXS:0010007_0016019 + MimsFoodFarmEnvironment: + name: MimsFoodFarmEnvironment + description: MIxS data that complies with the Mims checklist and the FoodFarmEnvironment + Extension + title: Mims combined with FoodFarmEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFarmEnvironment + mixins: + - Mims + class_uri: MIXS:0010007_0016020 + MimsFoodFoodProductionFacility: + name: MimsFoodFoodProductionFacility + description: MIxS data that complies with the Mims checklist and the FoodFoodProductionFacility + Extension + title: Mims combined with FoodFoodProductionFacility + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFoodProductionFacility + mixins: + - Mims + class_uri: MIXS:0010007_0016021 + MimsFoodHumanFoods: + name: MimsFoodHumanFoods + description: MIxS data that complies with the Mims checklist and the FoodHumanFoods + Extension + title: Mims combined with FoodHumanFoods + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodHumanFoods + mixins: + - Mims + class_uri: MIXS:0010007_0016022 + MimsHostAssociated: + name: MimsHostAssociated + description: MIxS data that complies with the Mims checklist and the HostAssociated + Extension + title: Mims combined with HostAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HostAssociated + mixins: + - Mims + class_uri: MIXS:0010007_0016002 + MimsHumanAssociated: + name: MimsHumanAssociated + description: MIxS data that complies with the Mims checklist and the HumanAssociated + Extension + title: Mims combined with HumanAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanAssociated + mixins: + - Mims + class_uri: MIXS:0010007_0016003 + MimsHumanGut: + name: MimsHumanGut + description: MIxS data that complies with the Mims checklist and the HumanGut + Extension + title: Mims combined with HumanGut + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanGut + mixins: + - Mims + class_uri: MIXS:0010007_0016004 + MimsHumanOral: + name: MimsHumanOral + description: MIxS data that complies with the Mims checklist and the HumanOral + Extension + title: Mims combined with HumanOral + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanOral + mixins: + - Mims + class_uri: MIXS:0010007_0016005 + MimsHumanSkin: + name: MimsHumanSkin + description: MIxS data that complies with the Mims checklist and the HumanSkin + Extension + title: Mims combined with HumanSkin + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanSkin + mixins: + - Mims + class_uri: MIXS:0010007_0016006 + MimsHumanVaginal: + name: MimsHumanVaginal + description: MIxS data that complies with the Mims checklist and the HumanVaginal + Extension + title: Mims combined with HumanVaginal + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanVaginal + mixins: + - Mims + class_uri: MIXS:0010007_0016007 + MimsHydrocarbonResourcesCores: + name: MimsHydrocarbonResourcesCores + description: MIxS data that complies with the Mims checklist and the HydrocarbonResourcesCores + Extension + title: Mims combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesCores + mixins: + - Mims + class_uri: MIXS:0010007_0016015 + MimsHydrocarbonResourcesFluidsSwabs: + name: MimsHydrocarbonResourcesFluidsSwabs + description: MIxS data that complies with the Mims checklist and the HydrocarbonResourcesFluidsSwabs + Extension + title: Mims combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - Mims + class_uri: MIXS:0010007_0016016 + MimsMicrobialMatBiofilm: + name: MimsMicrobialMatBiofilm + description: MIxS data that complies with the Mims checklist and the MicrobialMatBiofilm + Extension + title: Mims combined with MicrobialMatBiofilm + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MicrobialMatBiofilm + mixins: + - Mims + class_uri: MIXS:0010007_0016008 + MimsMiscellaneousNaturalOrArtificialEnvironment: + name: MimsMiscellaneousNaturalOrArtificialEnvironment + description: MIxS data that complies with the Mims checklist and the MiscellaneousNaturalOrArtificialEnvironment + Extension + title: Mims combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - Mims + class_uri: MIXS:0010007_0016009 + MimsPlantAssociated: + name: MimsPlantAssociated + description: MIxS data that complies with the Mims checklist and the PlantAssociated + Extension + title: Mims combined with PlantAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: PlantAssociated + mixins: + - Mims + class_uri: MIXS:0010007_0016010 + MimsSediment: + name: MimsSediment + description: MIxS data that complies with the Mims checklist and the Sediment + Extension + title: Mims combined with Sediment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Sediment + mixins: + - Mims + class_uri: MIXS:0010007_0016011 + MimsSoil: + name: MimsSoil + description: MIxS data that complies with the Mims checklist and the Soil Extension + title: Mims combined with Soil + in_subset: + - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - is_a: Extension - slots: - - samp_name - - project_name - - depth - - elev - - alkalinity - - alkalinity_method - - alkyl_diethers - - aminopept_act - - ammonium - - atmospheric_data - - bacteria_carb_prod - - bac_prod - - bac_resp - - biomass - - bishomohopanol - - bromide - - calcium - - carb_nitro_ratio - - chem_administration - - chloride - - chlorophyll - - conduc - - density - - diether_lipids - - diss_carb_dioxide - - diss_hydrogen - - diss_inorg_carb - - diss_inorg_nitro - - diss_inorg_phosp - - diss_org_carb - - diss_org_nitro - - diss_oxygen - - down_par - - fluor - - glucosidase_act - - light_intensity - - magnesium - - mean_frict_vel - - mean_peak_frict_vel - - misc_param - - n_alkanes - - nitrate - - nitrite - - nitro - - org_carb - - org_matter - - org_nitro - - organism_count - - oxy_stat_samp - - ph - - part_org_carb - - part_org_nitro - - perturbation - - petroleum_hydrocarb - - phaeopigments - - phosphate - - phosplipid_fatt_acid - - photon_flux - - potassium - - pressure - - primary_prod - - redox_potential - - salinity - - samp_store_dur - - samp_store_loc - - samp_store_temp - - samp_vol_we_dna_ext - - silicate - - size_frac_low - - size_frac_up - - sodium - - soluble_react_phosp - - sulfate - - sulfide - - suspend_part_matter - - temp - - tidal_stage - - tot_depth_water_col - - tot_diss_nitro - - tot_inorg_nitro - - tot_nitro - - tot_part_carb - - tot_phosp - - turbidity - - water_current - slot_usage: - alkyl_diethers: - name: alkyl_diethers - ammonium: - name: ammonium - required: false - recommended: false - bacteria_carb_prod: - name: bacteria_carb_prod - chem_administration: - name: chem_administration - required: false - recommended: false - depth: - name: depth - examples: - - value: 10 meter - required: true - diss_inorg_phosp: - name: diss_inorg_phosp - required: false - recommended: false - diss_org_nitro: - name: diss_org_nitro - elev: - name: elev - recommended: true - n_alkanes: - name: n_alkanes - nitrate: - name: nitrate - required: false - recommended: false - nitrite: - name: nitrite - required: false - recommended: false - org_carb: - name: org_carb - org_nitro: - name: org_nitro - organism_count: - name: organism_count - examples: - - value: total prokaryotes;3.5e7 cells per milliliter;qPCR - required: false - recommended: false - oxy_stat_samp: - name: oxy_stat_samp - required: false - recommended: false - part_org_carb: - name: part_org_carb - perturbation: - name: perturbation - required: false - recommended: false - ph: - name: ph - required: false - recommended: false - phosplipid_fatt_acid: - name: phosplipid_fatt_acid - samp_store_dur: - name: samp_store_dur - required: false - recommended: false - samp_store_loc: - name: samp_store_loc - required: false - recommended: false - samp_vol_we_dna_ext: - name: samp_vol_we_dna_ext - required: false - recommended: false - sulfate: - name: sulfate - required: false - recommended: false - sulfide: - name: sulfide - required: false - recommended: false - temp: - name: temp - required: false - recommended: false - turbidity: - name: turbidity - class_uri: MIXS:0016014 - Checklist: - name: Checklist - description: A collection of metadata terms (slots) to minimally describe the - sampling and sequencing method of a specimen used to generate a nucleotide sequence. + is_a: Soil + mixins: + - Mims + class_uri: MIXS:0010007_0016012 + MimsSymbiontAssociated: + name: MimsSymbiontAssociated + description: MIxS data that complies with the Mims checklist and the SymbiontAssociated + Extension + title: Mims combined with SymbiontAssociated + in_subset: + - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - Extension: - name: Extension - description: A collection of recommended metadata terms (slots) developed by community - experts, describing the specific context under which a sample was collected. + is_a: SymbiontAssociated + mixins: + - Mims + class_uri: MIXS:0010007_0016023 + MimsWastewaterSludge: + name: MimsWastewaterSludge + description: MIxS data that complies with the Mims checklist and the WastewaterSludge + Extension + title: Mims combined with WastewaterSludge + in_subset: + - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - aliases: - - EnvironmentalPackage - MixsCompliantData: - name: MixsCompliantData - description: A collection of data that complies with some combination of a MIxS - checklist and environmental extension - title: MIxS compliant data + is_a: WastewaterSludge + mixins: + - Mims + class_uri: MIXS:0010007_0016013 + MimsWater: + name: MimsWater + description: MIxS data that complies with the Mims checklist and the Water Extension + title: Mims combined with Water + in_subset: + - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - slots: - - migs_eu_data - - plant_associated_data - - migs_eu_plant_associated_data - - host_associated_data - - migs_eu_host_associated_data - - human_associated_data - - migs_eu_human_associated_data - - human_gut_data - - migs_eu_human_gut_data - - human_oral_data - - migs_eu_human_oral_data - - soil_data - - migs_eu_soil_data - - water_data - - migs_eu_water_data - - mims_data - - mims_plant_associated_data - - mims_host_associated_data - - mims_human_associated_data - - mims_human_gut_data - - mims_human_oral_data - - mims_soil_data - - mims_water_data - - mimarks_s_data - - mimarks_s_plant_associated_data - - mimarks_s_host_associated_data - - mimarks_s_human_associated_data - - mimarks_s_human_gut_data - - mimarks_s_human_oral_data - - mimarks_s_soil_data - - mimarks_s_water_data - tree_root: true - MigsEuPlantAssociated: - name: MigsEuPlantAssociated - description: MIxS data that complies with the MigsEu checklist and the PlantAssociated + is_a: Water + mixins: + - Mims + class_uri: MIXS:0010007_0016014 + MisagAgriculture: + name: MisagAgriculture + description: MIxS data that complies with the Misag checklist and the Agriculture + Extension + title: Misag combined with Agriculture + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Agriculture + mixins: + - Misag + class_uri: MIXS:0010010_0016018 + MisagAir: + name: MisagAir + description: MIxS data that complies with the Misag checklist and the Air Extension + title: Misag combined with Air + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Air + mixins: + - Misag + class_uri: MIXS:0010010_0016000 + MisagBuiltEnvironment: + name: MisagBuiltEnvironment + description: MIxS data that complies with the Misag checklist and the BuiltEnvironment Extension - title: MigsEu combined with PlantAssociated + title: Misag combined with BuiltEnvironment in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - is_a: PlantAssociated + is_a: BuiltEnvironment mixins: - - MigsEu - class_uri: MIXS:0010002_0016010 - MigsEuHostAssociated: - name: MigsEuHostAssociated - description: MIxS data that complies with the MigsEu checklist and the HostAssociated + - Misag + class_uri: MIXS:0010010_0016001 + MisagFoodAnimalAndAnimalFeed: + name: MisagFoodAnimalAndAnimalFeed + description: MIxS data that complies with the Misag checklist and the FoodAnimalAndAnimalFeed Extension - title: MigsEu combined with HostAssociated + title: Misag combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodAnimalAndAnimalFeed + mixins: + - Misag + class_uri: MIXS:0010010_0016019 + MisagFoodFarmEnvironment: + name: MisagFoodFarmEnvironment + description: MIxS data that complies with the Misag checklist and the FoodFarmEnvironment + Extension + title: Misag combined with FoodFarmEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFarmEnvironment + mixins: + - Misag + class_uri: MIXS:0010010_0016020 + MisagFoodFoodProductionFacility: + name: MisagFoodFoodProductionFacility + description: MIxS data that complies with the Misag checklist and the FoodFoodProductionFacility + Extension + title: Misag combined with FoodFoodProductionFacility + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFoodProductionFacility + mixins: + - Misag + class_uri: MIXS:0010010_0016021 + MisagFoodHumanFoods: + name: MisagFoodHumanFoods + description: MIxS data that complies with the Misag checklist and the FoodHumanFoods + Extension + title: Misag combined with FoodHumanFoods + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodHumanFoods + mixins: + - Misag + class_uri: MIXS:0010010_0016022 + MisagHostAssociated: + name: MisagHostAssociated + description: MIxS data that complies with the Misag checklist and the HostAssociated + Extension + title: Misag combined with HostAssociated in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc is_a: HostAssociated mixins: - - MigsEu - class_uri: MIXS:0010002_0016002 - MigsEuHumanAssociated: - name: MigsEuHumanAssociated - description: MIxS data that complies with the MigsEu checklist and the HumanAssociated + - Misag + class_uri: MIXS:0010010_0016002 + MisagHumanAssociated: + name: MisagHumanAssociated + description: MIxS data that complies with the Misag checklist and the HumanAssociated Extension - title: MigsEu combined with HumanAssociated + title: Misag combined with HumanAssociated in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc is_a: HumanAssociated mixins: - - MigsEu - class_uri: MIXS:0010002_0016003 - MigsEuHumanGut: - name: MigsEuHumanGut - description: MIxS data that complies with the MigsEu checklist and the HumanGut + - Misag + class_uri: MIXS:0010010_0016003 + MisagHumanGut: + name: MisagHumanGut + description: MIxS data that complies with the Misag checklist and the HumanGut Extension - title: MigsEu combined with HumanGut + title: Misag combined with HumanGut in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc is_a: HumanGut mixins: - - MigsEu - class_uri: MIXS:0010002_0016004 - MigsEuHumanOral: - name: MigsEuHumanOral - description: MIxS data that complies with the MigsEu checklist and the HumanOral + - Misag + class_uri: MIXS:0010010_0016004 + MisagHumanOral: + name: MisagHumanOral + description: MIxS data that complies with the Misag checklist and the HumanOral Extension - title: MigsEu combined with HumanOral + title: Misag combined with HumanOral in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc is_a: HumanOral mixins: - - MigsEu - class_uri: MIXS:0010002_0016005 - MigsEuSoil: - name: MigsEuSoil - description: MIxS data that complies with the MigsEu checklist and the Soil Extension - title: MigsEu combined with Soil + - Misag + class_uri: MIXS:0010010_0016005 + MisagHumanSkin: + name: MisagHumanSkin + description: MIxS data that complies with the Misag checklist and the HumanSkin + Extension + title: Misag combined with HumanSkin in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - is_a: Soil + is_a: HumanSkin mixins: - - MigsEu - class_uri: MIXS:0010002_0016012 - MigsEuWater: - name: MigsEuWater - description: MIxS data that complies with the MigsEu checklist and the Water Extension - title: MigsEu combined with Water + - Misag + class_uri: MIXS:0010010_0016006 + MisagHumanVaginal: + name: MisagHumanVaginal + description: MIxS data that complies with the Misag checklist and the HumanVaginal + Extension + title: Misag combined with HumanVaginal in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - is_a: Water + is_a: HumanVaginal mixins: - - MigsEu - class_uri: MIXS:0010002_0016014 - MimsPlantAssociated: - name: MimsPlantAssociated - description: MIxS data that complies with the Mims checklist and the PlantAssociated + - Misag + class_uri: MIXS:0010010_0016007 + MisagHydrocarbonResourcesCores: + name: MisagHydrocarbonResourcesCores + description: MIxS data that complies with the Misag checklist and the HydrocarbonResourcesCores Extension - title: Mims combined with PlantAssociated + title: Misag combined with HydrocarbonResourcesCores in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - is_a: PlantAssociated + is_a: HydrocarbonResourcesCores mixins: - - Mims - class_uri: MIXS:0010007_0016010 - MimsHostAssociated: - name: MimsHostAssociated - description: MIxS data that complies with the Mims checklist and the HostAssociated + - Misag + class_uri: MIXS:0010010_0016015 + MisagHydrocarbonResourcesFluidsSwabs: + name: MisagHydrocarbonResourcesFluidsSwabs + description: MIxS data that complies with the Misag checklist and the HydrocarbonResourcesFluidsSwabs Extension - title: Mims combined with HostAssociated + title: Misag combined with HydrocarbonResourcesFluidsSwabs in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - is_a: HostAssociated + is_a: HydrocarbonResourcesFluidsSwabs mixins: - - Mims - class_uri: MIXS:0010007_0016002 - MimsHumanAssociated: - name: MimsHumanAssociated - description: MIxS data that complies with the Mims checklist and the HumanAssociated + - Misag + class_uri: MIXS:0010010_0016016 + MisagMicrobialMatBiofilm: + name: MisagMicrobialMatBiofilm + description: MIxS data that complies with the Misag checklist and the MicrobialMatBiofilm Extension - title: Mims combined with HumanAssociated + title: Misag combined with MicrobialMatBiofilm in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - is_a: HumanAssociated + is_a: MicrobialMatBiofilm mixins: - - Mims - class_uri: MIXS:0010007_0016003 - MimsHumanGut: - name: MimsHumanGut - description: MIxS data that complies with the Mims checklist and the HumanGut + - Misag + class_uri: MIXS:0010010_0016008 + MisagMiscellaneousNaturalOrArtificialEnvironment: + name: MisagMiscellaneousNaturalOrArtificialEnvironment + description: MIxS data that complies with the Misag checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension - title: Mims combined with HumanGut + title: Misag combined with MiscellaneousNaturalOrArtificialEnvironment in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - is_a: HumanGut + is_a: MiscellaneousNaturalOrArtificialEnvironment mixins: - - Mims - class_uri: MIXS:0010007_0016004 - MimsHumanOral: - name: MimsHumanOral - description: MIxS data that complies with the Mims checklist and the HumanOral + - Misag + class_uri: MIXS:0010010_0016009 + MisagPlantAssociated: + name: MisagPlantAssociated + description: MIxS data that complies with the Misag checklist and the PlantAssociated Extension - title: Mims combined with HumanOral + title: Misag combined with PlantAssociated in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - is_a: HumanOral + is_a: PlantAssociated mixins: - - Mims - class_uri: MIXS:0010007_0016005 - MimsSoil: - name: MimsSoil - description: MIxS data that complies with the Mims checklist and the Soil Extension - title: Mims combined with Soil + - Misag + class_uri: MIXS:0010010_0016010 + MisagSediment: + name: MisagSediment + description: MIxS data that complies with the Misag checklist and the Sediment + Extension + title: Misag combined with Sediment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Sediment + mixins: + - Misag + class_uri: MIXS:0010010_0016011 + MisagSoil: + name: MisagSoil + description: MIxS data that complies with the Misag checklist and the Soil Extension + title: Misag combined with Soil in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc is_a: Soil mixins: - - Mims - class_uri: MIXS:0010007_0016012 - MimsWater: - name: MimsWater - description: MIxS data that complies with the Mims checklist and the Water Extension - title: Mims combined with Water + - Misag + class_uri: MIXS:0010010_0016012 + MisagSymbiontAssociated: + name: MisagSymbiontAssociated + description: MIxS data that complies with the Misag checklist and the SymbiontAssociated + Extension + title: Misag combined with SymbiontAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: SymbiontAssociated + mixins: + - Misag + class_uri: MIXS:0010010_0016023 + MisagWastewaterSludge: + name: MisagWastewaterSludge + description: MIxS data that complies with the Misag checklist and the WastewaterSludge + Extension + title: Misag combined with WastewaterSludge + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: WastewaterSludge + mixins: + - Misag + class_uri: MIXS:0010010_0016013 + MisagWater: + name: MisagWater + description: MIxS data that complies with the Misag checklist and the Water Extension + title: Misag combined with Water in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc is_a: Water mixins: - - Mims - class_uri: MIXS:0010007_0016014 - MimarksSPlantAssociated: - name: MimarksSPlantAssociated - description: MIxS data that complies with the MimarksS checklist and the PlantAssociated + - Misag + class_uri: MIXS:0010010_0016014 + MiuvigAgriculture: + name: MiuvigAgriculture + description: MIxS data that complies with the Miuvig checklist and the Agriculture Extension - title: MimarksS combined with PlantAssociated + title: Miuvig combined with Agriculture in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc - is_a: PlantAssociated + is_a: Agriculture mixins: - - MimarksS - class_uri: MIXS:0010008_0016010 - MimarksSHostAssociated: - name: MimarksSHostAssociated - description: MIxS data that complies with the MimarksS checklist and the HostAssociated + - Miuvig + class_uri: MIXS:0010012_0016018 + MiuvigAir: + name: MiuvigAir + description: MIxS data that complies with the Miuvig checklist and the Air Extension + title: Miuvig combined with Air + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Air + mixins: + - Miuvig + class_uri: MIXS:0010012_0016000 + MiuvigBuiltEnvironment: + name: MiuvigBuiltEnvironment + description: MIxS data that complies with the Miuvig checklist and the BuiltEnvironment Extension - title: MimarksS combined with HostAssociated + title: Miuvig combined with BuiltEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: BuiltEnvironment + mixins: + - Miuvig + class_uri: MIXS:0010012_0016001 + MiuvigFoodAnimalAndAnimalFeed: + name: MiuvigFoodAnimalAndAnimalFeed + description: MIxS data that complies with the Miuvig checklist and the FoodAnimalAndAnimalFeed + Extension + title: Miuvig combined with FoodAnimalAndAnimalFeed + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodAnimalAndAnimalFeed + mixins: + - Miuvig + class_uri: MIXS:0010012_0016019 + MiuvigFoodFarmEnvironment: + name: MiuvigFoodFarmEnvironment + description: MIxS data that complies with the Miuvig checklist and the FoodFarmEnvironment + Extension + title: Miuvig combined with FoodFarmEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFarmEnvironment + mixins: + - Miuvig + class_uri: MIXS:0010012_0016020 + MiuvigFoodFoodProductionFacility: + name: MiuvigFoodFoodProductionFacility + description: MIxS data that complies with the Miuvig checklist and the FoodFoodProductionFacility + Extension + title: Miuvig combined with FoodFoodProductionFacility + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodFoodProductionFacility + mixins: + - Miuvig + class_uri: MIXS:0010012_0016021 + MiuvigFoodHumanFoods: + name: MiuvigFoodHumanFoods + description: MIxS data that complies with the Miuvig checklist and the FoodHumanFoods + Extension + title: Miuvig combined with FoodHumanFoods + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: FoodHumanFoods + mixins: + - Miuvig + class_uri: MIXS:0010012_0016022 + MiuvigHostAssociated: + name: MiuvigHostAssociated + description: MIxS data that complies with the Miuvig checklist and the HostAssociated + Extension + title: Miuvig combined with HostAssociated in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc is_a: HostAssociated mixins: - - MimarksS - class_uri: MIXS:0010008_0016002 - MimarksSHumanAssociated: - name: MimarksSHumanAssociated - description: MIxS data that complies with the MimarksS checklist and the HumanAssociated + - Miuvig + class_uri: MIXS:0010012_0016002 + MiuvigHumanAssociated: + name: MiuvigHumanAssociated + description: MIxS data that complies with the Miuvig checklist and the HumanAssociated Extension - title: MimarksS combined with HumanAssociated + title: Miuvig combined with HumanAssociated in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc is_a: HumanAssociated mixins: - - MimarksS - class_uri: MIXS:0010008_0016003 - MimarksSHumanGut: - name: MimarksSHumanGut - description: MIxS data that complies with the MimarksS checklist and the HumanGut + - Miuvig + class_uri: MIXS:0010012_0016003 + MiuvigHumanGut: + name: MiuvigHumanGut + description: MIxS data that complies with the Miuvig checklist and the HumanGut Extension - title: MimarksS combined with HumanGut + title: Miuvig combined with HumanGut in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc is_a: HumanGut mixins: - - MimarksS - class_uri: MIXS:0010008_0016004 - MimarksSHumanOral: - name: MimarksSHumanOral - description: MIxS data that complies with the MimarksS checklist and the HumanOral + - Miuvig + class_uri: MIXS:0010012_0016004 + MiuvigHumanOral: + name: MiuvigHumanOral + description: MIxS data that complies with the Miuvig checklist and the HumanOral Extension - title: MimarksS combined with HumanOral + title: Miuvig combined with HumanOral in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc is_a: HumanOral mixins: - - MimarksS - class_uri: MIXS:0010008_0016005 - MimarksSSoil: - name: MimarksSSoil - description: MIxS data that complies with the MimarksS checklist and the Soil + - Miuvig + class_uri: MIXS:0010012_0016005 + MiuvigHumanSkin: + name: MiuvigHumanSkin + description: MIxS data that complies with the Miuvig checklist and the HumanSkin Extension - title: MimarksS combined with Soil + title: Miuvig combined with HumanSkin + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanSkin + mixins: + - Miuvig + class_uri: MIXS:0010012_0016006 + MiuvigHumanVaginal: + name: MiuvigHumanVaginal + description: MIxS data that complies with the Miuvig checklist and the HumanVaginal + Extension + title: Miuvig combined with HumanVaginal + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HumanVaginal + mixins: + - Miuvig + class_uri: MIXS:0010012_0016007 + MiuvigHydrocarbonResourcesCores: + name: MiuvigHydrocarbonResourcesCores + description: MIxS data that complies with the Miuvig checklist and the HydrocarbonResourcesCores + Extension + title: Miuvig combined with HydrocarbonResourcesCores + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesCores + mixins: + - Miuvig + class_uri: MIXS:0010012_0016015 + MiuvigHydrocarbonResourcesFluidsSwabs: + name: MiuvigHydrocarbonResourcesFluidsSwabs + description: MIxS data that complies with the Miuvig checklist and the HydrocarbonResourcesFluidsSwabs + Extension + title: Miuvig combined with HydrocarbonResourcesFluidsSwabs + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: HydrocarbonResourcesFluidsSwabs + mixins: + - Miuvig + class_uri: MIXS:0010012_0016016 + MiuvigMicrobialMatBiofilm: + name: MiuvigMicrobialMatBiofilm + description: MIxS data that complies with the Miuvig checklist and the MicrobialMatBiofilm + Extension + title: Miuvig combined with MicrobialMatBiofilm + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MicrobialMatBiofilm + mixins: + - Miuvig + class_uri: MIXS:0010012_0016008 + MiuvigMiscellaneousNaturalOrArtificialEnvironment: + name: MiuvigMiscellaneousNaturalOrArtificialEnvironment + description: MIxS data that complies with the Miuvig checklist and the MiscellaneousNaturalOrArtificialEnvironment + Extension + title: Miuvig combined with MiscellaneousNaturalOrArtificialEnvironment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: MiscellaneousNaturalOrArtificialEnvironment + mixins: + - Miuvig + class_uri: MIXS:0010012_0016009 + MiuvigPlantAssociated: + name: MiuvigPlantAssociated + description: MIxS data that complies with the Miuvig checklist and the PlantAssociated + Extension + title: Miuvig combined with PlantAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: PlantAssociated + mixins: + - Miuvig + class_uri: MIXS:0010012_0016010 + MiuvigSediment: + name: MiuvigSediment + description: MIxS data that complies with the Miuvig checklist and the Sediment + Extension + title: Miuvig combined with Sediment + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: Sediment + mixins: + - Miuvig + class_uri: MIXS:0010012_0016011 + MiuvigSoil: + name: MiuvigSoil + description: MIxS data that complies with the Miuvig checklist and the Soil Extension + title: Miuvig combined with Soil in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc is_a: Soil mixins: - - MimarksS - class_uri: MIXS:0010008_0016012 - MimarksSWater: - name: MimarksSWater - description: MIxS data that complies with the MimarksS checklist and the Water + - Miuvig + class_uri: MIXS:0010012_0016012 + MiuvigSymbiontAssociated: + name: MiuvigSymbiontAssociated + description: MIxS data that complies with the Miuvig checklist and the SymbiontAssociated Extension - title: MimarksS combined with Water + title: Miuvig combined with SymbiontAssociated + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: SymbiontAssociated + mixins: + - Miuvig + class_uri: MIXS:0010012_0016023 + MiuvigWastewaterSludge: + name: MiuvigWastewaterSludge + description: MIxS data that complies with the Miuvig checklist and the WastewaterSludge + Extension + title: Miuvig combined with WastewaterSludge + in_subset: + - combination_classes + from_schema: https://w3id.org/mixs-6-2-rc + is_a: WastewaterSludge + mixins: + - Miuvig + class_uri: MIXS:0010012_0016013 + MiuvigWater: + name: MiuvigWater + description: MIxS data that complies with the Miuvig checklist and the Water Extension + title: Miuvig combined with Water in_subset: - combination_classes from_schema: https://w3id.org/mixs-6-2-rc is_a: Water mixins: - - MimarksS - class_uri: MIXS:0010008_0016014 + - Miuvig + class_uri: MIXS:0010012_0016014 source_file: generated-schema/mixs_6_2_rc.yaml.notated.yaml settings: country: