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core.yaml
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core.yaml
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id: https://w3id.org/nmdc/core
name: NMDC-Core
title: NMDC Schema Core Types
description: Schema for National Microbiome Data Collaborative (NMDC), Core Types
comments:
- includes all elements that were recently in prov.yaml
license: https://creativecommons.org/publicdomain/zero/1.0/
imports:
- attribute_values
- portal_emsl
- portal_jgi_metagenomics
- portal_jgi_metatranscriptomics
- portal_mixs_inspired
- portal_sample_id
prefixes:
CHEBI: http://purl.obolibrary.org/obo/CHEBI_
KEGG.COMPOUND: "https://bioregistry.io/kegg.compound:"
OBI: http://purl.obolibrary.org/obo/OBI_
PR: http://purl.obolibrary.org/obo/PR_
SIO: http://semanticscience.org/resource/SIO_
UniProtKB: "https://bioregistry.io/uniprot:"
biolink: https://w3id.org/biolink/vocab/
dcterms: http://purl.org/dc/terms/
linkml: https://w3id.org/linkml/
nmdc: https://w3id.org/nmdc/
prov: http://www.w3.org/ns/prov#
qud: http://qudt.org/1.1/schema/qudt#
rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
schema: http://schema.org/
wgs84: http://www.w3.org/2003/01/geo/wgs84_pos#
MISO: http://purl.obolibrary.org/obo/MISO_
default_prefix: nmdc
default_range: string
enums:
ChemicalConversionCategoryEnum:
permissible_values:
addition:
substitution:
acid_base:
reduction_oxidation:
combustion:
decomposition:
protease_cleavage:
description: an enzymatic cleavage which relies on an enzyme with protease activity to act on proteins and to produce polypeptides (protein fragments).
meaning: OBI:0600056
BiosampleCategoryEnum:
description: Funding-based, sample location-based, or experimental method-based defined categories
aliases:
- category tag
notes:
- Currently, these values can associated with biosamples via the biosample_categories slot
- They might also be applicable to other classes
- They are intended to enable metadata search and or filtering, for example in the NMDC data portal, https://data.microbiomedata.org/
permissible_values:
LTER:
title: National Science Foundation's Long Term Ecological Research Network
meaning: https://lternet.edu/
SIP: { }
SFA:
title: Department of Energy Office of Science Biological and Environmental Research Program Laboratory Science Focus Areas
description: Science Focus Area projects funded through the Department of Energy Office of Science Biological and Environmental Research Program
meaning: https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance
FICUS:
title: Facilities Integrating Collaborations for User Science
meaning: https://jgi.doe.gov/user-programs/program-info/ficus-overview
NEON:
title: National Science Foundation's National Ecological Observatory Network
meaning: https://www.neonscience.org
SubstanceRoleEnum:
permissible_values:
buffer:
description: Maintains the pH of the solution within a specific range to stabilize analytes or reactions.
meaning: CHEBI:35225
acid:
description: Donates a proton or accepts an electron pair in a chemical reaction.
meaning: CHEBI:37527
base:
description: Accepts a proton or donates an electron pair in a chemical reaction.
meaning: CHEBI:22695
# protease:
# description: Enzyme that catalyzes cleavage of peptide bonds in proteins.
# proteolytic_enzyme:
# description: Enzyme that catalyzes the hydrolysis of proteins.
ms_proteolytic_enzyme:
description: Enzyme that catalyzes the hydrolysis of proteins and is used in mass spectrometry based proteomics
meaning: MS:1002986
solvent:
description: Dissolves the sample or reagents to facilitate reactions or extraction.
meaning: CHEBI:46787
surfactant:
description: Reduces surface tension and aids in the solubilization of substances.
meaning: CHEBI:35195
# stabilizer:
# description: Prevents degradation or loss of analytes during sample storage or preparation.
# meaning: CFo000000033
derivatizing_agent:
description: Chemically modifies analytes to improve detection or separation.
# meaning: MSIO:0000003
# labeling_reagent:
# description: Introduces a detectable label for tracing or quantification.
# precipitating_agent:
# description: Causes precipitation of unwanted substances or aids in the concentration of analytes.
solubilizing_agent: { }
SampleStateEnum:
permissible_values:
solid:
liquid:
gas:
classes:
ChemicalConversionProcess:
class_uri: 'nmdc:ChemicalConversionProcess'
aliases:
- chemical reaction
exact_mappings:
- MISO:0000001 # MaterialProcessing which uses or consumes chemical/molecular entities to generate other molecular entities
description: >
A process that results in the interconversion of chemical species by a reaction to transform the reagents into products.
contributors:
- ORCID:0009-0001-1555-1601 #Anastasiya Prymolenna
- ORCID:0000-0002-1368-8217 #Yuri Corilo
is_a: MaterialProcessing
comments:
- The values of both has_reagents slot and has_input slot are considered the reagents of a chemical process.
slots:
- chemical_conversion_category
- duration
- temperature
- substances_used
- substances_volume
slot_usage:
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$"
interpolated: true
MetagenomeAnnotation:
class_uri: nmdc:MetagenomeAnnotation
description: A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs
is_a: WorkflowExecution
slots:
- img_identifiers
- gold_analysis_project_identifiers
in_subset:
- workflow subset
slot_usage:
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$"
interpolated: true
img_identifiers:
maximum_cardinality: 1
was_informed_by:
structured_pattern:
syntax: "{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$"
interpolated: true
gold_analysis_project_identifiers:
structured_pattern:
syntax: "^gold:Ga[0-9]+$"
interpolated: true
FieldResearchSite:
class_uri: nmdc:FieldResearchSite
aliases:
- research plot
description: A site, outside of a laboratory, from which biosamples may be collected.
is_a: Site
title: Field Research Site
comments:
- Provides grouping of biosamples at level that's more specific than belonging
to the same study
- be very clear that this could be part of a larger site
- In Bioscales, one might say that rhizosphere soil and bulk soil from around
the same plant were obtained at the same site. In this case, the site would
correspond to one tree.
- "might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833"
slots:
- cur_vegetation
- elev
- geo_loc_name
- habitat # gold term... enumerated values?
- lat_lon
- local_class
- part_of
- soil_type
slot_usage:
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$"
interpolated: true
part_of:
range: FieldResearchSite
structured_pattern:
syntax: "{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$"
interpolated: true
Biosample:
class_uri: 'nmdc:Biosample'
rules:
- title: dna_well_requires_plate
description: DNA samples shipped to JGI for metagenomic analysis in tubes can't have any value for their plate position.
preconditions:
slot_conditions:
dna_cont_well:
pattern: ".+"
postconditions:
slot_conditions:
dna_cont_type:
equals_string: plate
- title: dna_plate_requires_well
description:
DNA samples in plates must have a plate position that matches the regex.
Note the requirement for an empty string in the tube case.
Waiting for value_present validation to be added to runtime
preconditions:
slot_conditions:
dna_cont_type:
equals_string: plate
postconditions:
slot_conditions:
dna_cont_well:
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
- title: rna_well_requires_plate
description: RNA samples shipped to JGI for metagenomic analysis in tubes can't have any value for their plate position.
preconditions:
slot_conditions:
rna_cont_well:
pattern: ".+"
postconditions:
slot_conditions:
rna_cont_type:
equals_string: plate
- title: rna_plate_requires_well
description:
RNA samples in plates must have a plate position that matches the regex.
Note the requirement for an empty string in the tube case.
Waiting for value_present validation to be added to runtime
preconditions:
slot_conditions:
rna_cont_type:
equals_string: plate
postconditions:
slot_conditions:
rna_cont_well:
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
unique_keys:
samp_name_unique_key:
unique_key_slots:
- samp_name # id is already required to be unique because it is the identifier in Biosample's parent class, NamedThing
is_a: MaterialEntity
in_subset:
- sample subset
aliases:
- sample
- material sample
- specimen
- biospecimen
description: >-
Biological source material which can be characterized by an experiment.
notes:
- could add GOLD and EBI's biosample definitions to the alt_descriptions?
alt_descriptions:
embl.ena:
A sample contains information about the sequenced source material.
Samples are associated with checklists, which define the fields used to annotate
the samples. Samples are always associated with a taxon.
slots:
- associated_studies
- biosample_categories
- collected_from
- embargoed
- host_disease_stat
- host_taxid
- img_identifiers
- neon_biosample_identifiers
- samp_name
## external IDs, alternate IDs
- gold_biosample_identifiers
- insdc_biosample_identifiers
- emsl_biosample_identifiers
- igsn_biosample_identifiers
## MIXS slots
- abs_air_humidity
- add_recov_method
- additional_info
- address
- adj_room
- aero_struc
- agrochem_addition
- air_PM_concen
- air_temp
- air_temp_regm
- al_sat
- al_sat_meth
- alkalinity
- alkalinity_method
- alkyl_diethers
- alt
- aminopept_act
- ammonium
- ammonium_nitrogen
- amount_light
- ances_data
- annual_precpt
- annual_temp
- antibiotic_regm
- api
- arch_struc
- aromatics_pc
- asphaltenes_pc
- atmospheric_data
- avg_dew_point
- avg_occup
- avg_temp
- bac_prod
- bac_resp
- bacteria_carb_prod
- barometric_press
- basin
- bathroom_count
- bedroom_count
- benzene
- biochem_oxygen_dem
- biocide
- biocide_admin_method
- biol_stat
- biomass
- biotic_regm
- biotic_relationship
- bishomohopanol
- blood_press_diast
- blood_press_syst
- bromide
- build_docs
- build_occup_type
- building_setting
- built_struc_age
- built_struc_set
- built_struc_type
- calcium
- carb_dioxide
- carb_monoxide
- carb_nitro_ratio
- ceil_area
- ceil_cond
- ceil_finish_mat
- ceil_struc
- ceil_texture
- ceil_thermal_mass
- ceil_type
- ceil_water_mold
- chem_administration
- chem_mutagen
- chem_oxygen_dem
- chem_treat_method
- chem_treatment
- chloride
- chlorophyll
- climate_environment
- collection_date
- conduc
- cool_syst_id
- core field
- crop_rotation
- cult_root_med
- cur_land_use
- cur_vegetation
- cur_vegetation_meth
- date_last_rain
- density
- depos_env
- depth
- dew_point
- diether_lipids
- diss_carb_dioxide
- diss_hydrogen
- diss_inorg_carb
- diss_inorg_nitro
- diss_inorg_phosp
- diss_iron
- diss_org_carb
- diss_org_nitro
- diss_oxygen
- diss_oxygen_fluid
- dna_cont_well
- door_comp_type
- door_cond
- door_direct
- door_loc
- door_mat
- door_move
- door_size
- door_type
- door_type_metal
- door_type_wood
- door_water_mold
- down_par
- drainage_class
- drawings
- ecosystem
- ecosystem_category
- ecosystem_subtype
- ecosystem_type
- efficiency_percent
- elev
- elevator
- emulsions
- env_broad_scale
- env_local_scale
- env_medium
- env_package
- environment field
- escalator
- ethylbenzene
- exp_duct
- exp_pipe
- experimental_factor
- ext_door
- ext_wall_orient
- ext_window_orient
- extreme_event
- fao_class
- fertilizer_regm
- field
- filter_type
- fire
- fireplace_type
- flooding
- floor_age
- floor_area
- floor_cond
- floor_count
- floor_finish_mat
- floor_struc
- floor_thermal_mass
- floor_water_mold
- fluor
- freq_clean
- freq_cook
- fungicide_regm
- furniture
- gaseous_environment
- gaseous_substances
- gender_restroom
- genetic_mod
- geo_loc_name
- glucosidase_act
- gravidity
- gravity
- growth_facil
- growth_habit
- growth_hormone_regm
- hall_count
- handidness
- hc_produced
- hcr
- hcr_fw_salinity
- hcr_geol_age
- hcr_pressure
- hcr_temp
- heat_cool_type
- heat_deliv_loc
- heat_sys_deliv_meth
- heat_system_id
- heavy_metals
- heavy_metals_meth
- height_carper_fiber
- herbicide_regm
- horizon_meth
- host_age
- host_body_habitat
- host_body_product
- host_body_site
- host_body_temp
- host_color
- host_common_name
- host_diet
- host_dry_mass
- host_family_relation
- host_genotype
- host_growth_cond
- host_height
- host_last_meal
- host_length
- host_life_stage
- host_phenotype
- host_sex
- host_shape
- host_subject_id
- host_subspecf_genlin
- host_substrate
- host_symbiont
- host_taxid
- host_tot_mass
- host_wet_mass
- humidity
- humidity_regm
- indoor_space
- indoor_surf
- indust_eff_percent
- inorg_particles
- inside_lux
- int_wall_cond
- investigation field
- iw_bt_date_well
- iwf
- last_clean
- lat_lon
- lbc_thirty
- lbceq
- light_intensity
- light_regm
- light_type
- link_addit_analys
- link_class_info
- link_climate_info
- lithology
- local_class
- local_class_meth
- magnesium
- manganese
- max_occup
- mean_frict_vel
- mean_peak_frict_vel
- mech_struc
- mechanical_damage
- methane
- micro_biomass_meth
- microbial_biomass
- mineral_nutr_regm
- misc_param
- n_alkanes
- nitrate
- nitrate_nitrogen
- nitrite
- nitrite_nitrogen
- nitro
- non_min_nutr_regm
- nucleic acid sequence source field
- number_pets
- number_plants
- number_resident
- occup_density_samp
- occup_document
- occup_samp
- org_carb
- org_count_qpcr_info
- org_matter
- org_nitro
- org_particles
- organism_count
- owc_tvdss
- oxy_stat_samp
- oxygen
- part_org_carb
- part_org_nitro
- particle_class
- permeability
- perturbation
- pesticide_regm
- petroleum_hydrocarb
- ph
- ph_meth
- ph_regm
- phaeopigments
- phosphate
- phosplipid_fatt_acid
- photon_flux
- plant_growth_med
- plant_product
- plant_sex
- plant_struc
- pollutants
- porosity
- potassium
- pour_point
- pre_treatment
- pres_animal_insect
- pressure
- prev_land_use_meth
- previous_land_use
- primary_prod
- primary_treatment
- prod_rate
- prod_start_date
- profile_position
- quad_pos
- radiation_regm
- rainfall_regm
- reactor_type
- redox_potential
- rel_air_humidity
- rel_humidity_out
- rel_samp_loc
- reservoir
- resins_pc
- room_air_exch_rate
- room_architec_elem
- room_condt
- room_connected
- room_count
- room_dim
- room_door_dist
- room_door_share
- room_hallway
- room_loc
- room_moist_dam_hist
- room_net_area
- room_occup
- room_samp_pos
- room_type
- room_vol
- room_wall_share
- room_window_count
- root_cond
- root_med_carbon
- root_med_macronutr
- root_med_micronutr
- root_med_ph
- root_med_regl
- root_med_solid
- root_med_suppl
- salinity
- salinity_meth
- salt_regm
- samp_capt_status
- samp_collec_device
- samp_collec_method
- samp_collect_point
- samp_dis_stage
- samp_floor
- samp_loc_corr_rate
- samp_mat_process
- samp_md
- samp_name
- samp_preserv
- samp_room_id
- samp_size
- samp_sort_meth
- samp_store_dur
- samp_store_loc
- samp_store_temp
- samp_subtype
- samp_taxon_id
- samp_time_out
- samp_transport_cond
- samp_tvdss
- samp_type
- samp_weather
- samp_well_name
- saturates_pc
- season
- season_environment
- season_precpt
- season_temp
- season_use
- secondary_treatment
- sediment_type
- sequencing field
- sewage_type
- shad_dev_water_mold
- shading_device_cond
- shading_device_loc
- shading_device_mat
- shading_device_type
- sieving
- silicate
- size_frac
- size_frac_low
- size_frac_up
- slope_aspect
- slope_gradient
- sludge_retent_time
- sodium
- soil_horizon
- soil_text_measure
- soil_texture_meth
- soil_type
- soil_type_meth
- solar_irradiance
- soluble_inorg_mat
- soluble_org_mat
- soluble_react_phosp
- source_mat_id
- space_typ_state
- specific
- specific_ecosystem
- specific_humidity
- sr_dep_env
- sr_geol_age
- sr_kerog_type
- sr_lithology
- standing_water_regm
- store_cond
- substructure_type
- sulfate
- sulfate_fw
- sulfide
- surf_air_cont
- surf_humidity
- surf_material
- surf_moisture
- surf_moisture_ph
- surf_temp
- suspend_part_matter
- suspend_solids
- tan
- temp
- temp_out
- tertiary_treatment
- tidal_stage
- tillage
- tiss_cult_growth_med
- toluene
- tot_carb
- tot_depth_water_col
- tot_diss_nitro
- tot_inorg_nitro
- tot_iron
- tot_nitro
- tot_nitro_cont_meth
- tot_nitro_content
- tot_org_c_meth
- tot_org_carb
- tot_part_carb
- tot_phosp
- tot_phosphate
- tot_sulfur
- train_line
- train_stat_loc
- train_stop_loc
- turbidity
- tvdss_of_hcr_press
- tvdss_of_hcr_temp
- typ_occup_density
- ventilation_rate
- ventilation_type
- vfa
- vfa_fw
- vis_media
- viscosity
- volatile_org_comp
- wall_area
- wall_const_type
- wall_finish_mat
- wall_height
- wall_loc
- wall_surf_treatment
- wall_texture
- wall_thermal_mass
- wall_water_mold
- wastewater_type
- water_cont_soil_meth
- water_content
- water_current
- water_cut
- water_feat_size
- water_feat_type
- water_prod_rate
- water_temp_regm
- watering_regm
- weekday
- win
- wind_direction
- wind_speed
- window_cond
- window_cover
- window_horiz_pos
- window_loc
- window_mat
- window_open_freq
- window_size
- window_status
- window_type
- window_vert_pos
- window_water_mold
- xylene
- zinc
## GOLD path fields
- ecosystem
- ecosystem_category
- ecosystem_type
- ecosystem_subtype
- specific_ecosystem
## GOLD specific fields
- add_date
- community
- habitat
- host_name
- location
- mod_date
- ncbi_taxonomy_name
- proport_woa_temperature
- salinity_category
- sample_collection_site
- soluble_iron_micromol
- subsurface_depth
## MIxS terms initially used in
## sample metadata submission portal (aka DataHarmonizer)
- air_temp_regm
- biotic_regm
- biotic_relationship
- climate_environment
- experimental_factor
- gaseous_environment
- growth_facil
- humidity_regm
- light_regm
- phosphate
- samp_collec_method
- samp_size
- source_mat_id
- watering_regm
## sample metadata submission portal (aka DataHarmonizer) terms (EMSL, JGI, etc.)
## JGI fields
- dna_absorb1
- dna_absorb2
- dna_collect_site
- dna_concentration
- dna_cont_type
- dna_cont_well
- dna_container_id
- dna_dnase
- dna_isolate_meth
- dna_organisms
- dna_project_contact
- dna_samp_id
- dna_sample_format
- dna_sample_name
- dna_seq_project
- dna_seq_project_pi
- dna_seq_project_name
- dna_volume
- proposal_dna
- dnase_rna
- proposal_rna
- rna_absorb1
- rna_absorb2
- rna_collect_site
- rna_concentration
- rna_cont_type
- rna_cont_well
- rna_container_id
- rna_isolate_meth
- rna_organisms
- rna_project_contact
- rna_samp_id
- rna_sample_format
- rna_sample_name
- rna_seq_project
- rna_seq_project_pi
- rna_seq_project_name
- rna_volume
## MIxS Inspired fields
- collection_date_inc
- collection_time
- collection_time_inc
- experimental_factor_other
- filter_method
- isotope_exposure
- micro_biomass_c_meth
- micro_biomass_n_meth
- microbial_biomass_c
- microbial_biomass_n
- non_microb_biomass
- non_microb_biomass_method
- org_nitro_method
- other_treatment
- start_date_inc
- start_time_inc
- project_id
- replicate_number
- sample_shipped
- sample_type
- technical_reps
- analysis_type
- sample_link
## EMSL slots
- bulk_elect_conductivity
- infiltrations
## bioscales slots
- zinc
- manganese
- ammonium_nitrogen
- nitrate_nitrogen
- nitrite_nitrogen
- lbc_thirty
- lbceq
slot_usage:
collected_from:
structured_pattern:
syntax: "{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$"
interpolated: true
elev:
title: elevation, meters
range: float
comments:
- All elevations must be reported in meters. Provide the numerical portion only.
- Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,
if needed, to help estimate the elevation based on latitude and longitude coordinates.
examples:
value: 100
id:
required: true
description: An NMDC assigned unique identifier for a biosample submitted to NMDC.
structured_pattern:
syntax: "{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$"
interpolated: true
gold_biosample_identifiers:
description: Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample
comments: This is the ID provided by GOLD that starts with 'GB'
annotations:
tooltip: Provide the GOLD biosample IDs associated with this biosample.
alternative_identifiers:
description: Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC
lat_lon:
notes:
- This is currently a required field but it's not clear if this
should be required for human hosts
env_broad_scale:
required: true
env_local_scale:
required: true
env_medium:
required: true
associated_studies:
required: true
range: Study
structured_pattern:
syntax: "{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$"
interpolated: true
fire:
comments:
- Provide the date the fire occurred. If extended burning occurred provide the date range.
examples:
- value: 1871-10-10
- value: 1871-10-01 to 1871-10-31
todos:
- is "to" acceptable? Is there a better way to request that be written?
annotations:
expected_value: date string
range: string
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?(\s+to\s+[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?)?$
flooding:
annotations:
expected_value: date string
comments:
- Provide the date the flood occurred. If extended flooding occurred provide the date range.
examples:
- value: 1927-04-15
- value: 1927-04 to 1927-05
todos:
- is "to" acceptable? Is there a better way to request that be written?
- What about if the "day" isn't known? Is this ok?
range: string
extreme_event:
examples:
- value: 1980-05-18, volcanic eruption
annotations:
expected_value: date, string
range: string
slope_aspect:
examples:
- value: 35
comments:
- Aspect is the orientation of slope, measured clockwise in degrees from 0 to 360,
where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270 is west-facing.
description:
The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees).