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portal_mixs_inspired.yaml
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portal_mixs_inspired.yaml
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name: mixs_inspired
description: This file defines terms that appear in the 'MIxS Inspired' section of
the NMDC sample metadata submission portal, which is implemented with DataHarmonizer
as of Spring 2022
title: 'NMDC Schema supplement for Submission Portal: MIxS Inspired'
id: https://w3id.org/nmdc/portal/mixs_inspired
license: https://creativecommons.org/publicdomain/zero/1.0/
prefixes:
linkml: https://w3id.org/linkml/
nmdc: https://w3id.org/nmdc/
MIXS: https://w3id.org/mixs/
imports:
- nmdc_types
default_prefix: nmdc
default_range: string
slots:
collection_date_inc:
description: Date the incubation was harvested/collected/ended. Only relevant
for incubation samples.
title: incubation collection date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
date only
comments:
- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
are all acceptable.
examples:
- value: 2021-04-15, 2021-04 and 2021 are all acceptable.
see_also:
- MIXS:0000011
rank: 2
string_serialization: '{date, arbitrary precision}'
slot_group: MIxS Inspired
recommended: true
collection_time:
description: The time of sampling, either as an instance (single point) or interval.
title: collection time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
see_also:
- MIXS:0000011
rank: 1
string_serialization: '{time, seconds optional}'
slot_group: MIxS Inspired
recommended: true
collection_time_inc:
description: Time the incubation was harvested/collected/ended. Only relevant
for incubation samples.
title: incubation collection time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
see_also:
- MIXS:0000011
rank: 3
string_serialization: '{time, seconds optional}'
slot_group: MIxS Inspired
recommended: true
experimental_factor_other:
description: Other details about your sample that you feel can't be accurately
represented in the available columns.
title: experimental factor- other
comments:
- This slot accepts open-ended text about your sample.
- We recommend using key:value pairs.
- Provided pairs will be considered for inclusion as future slots/terms in this
data collection template.
examples:
- value: 'experimental treatment: value'
see_also:
- MIXS:0000008
- MIXS:0000300
rank: 7
string_serialization: '{text}'
slot_group: MIxS Inspired
recommended: true
filter_method:
description: Type of filter used or how the sample was filtered
title: filter method
comments:
- describe the filter or provide a catalog number and manufacturer
examples:
- value: C18
- value: Basix PES, 13-100-106 FisherSci
see_also:
- MIXS:0000765
rank: 6
string_serialization: '{text}'
slot_group: MIxS Inspired
recommended: true
isotope_exposure:
description: List isotope exposure or addition applied to your sample.
title: isotope exposure/addition
todos:
- Can we make the H218O correctly super and subscripted?
comments:
- This is required when your experimental design includes the use of isotopically
labeled compounds
examples:
- value: 13C glucose
- value: H218O
see_also:
- MIXS:0000751
rank: 16
string_serialization: '{termLabel} {[termID]}; {timestamp}'
slot_group: MIxS Inspired
recommended: true
micro_biomass_c_meth:
description: Reference or method used in determining microbial biomass carbon
title: microbial biomass carbon method
todos:
- How should we separate values? | or ;? lets be consistent
comments:
- required if "microbial_biomass_c" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(87)90052-6
- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526
see_also:
- MIXS:0000339
rank: 11
string_serialization: '{PMID}|{DOI}|{URL}'
slot_group: MIxS Inspired
recommended: true
micro_biomass_n_meth:
description: Reference or method used in determining microbial biomass nitrogen
title: microbial biomass nitrogen method
comments:
- required if "microbial_biomass_n" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(87)90052-6
- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526
see_also:
- MIXS:0000339
rank: 13
string_serialization: '{PMID}|{DOI}|{URL}'
slot_group: MIxS Inspired
microbial_biomass_c:
description: The part of the organic matter in the soil that constitutes living
microorganisms smaller than 5-10 micrometer.
title: microbial biomass carbon
comments:
- If you provide this, correction factors used for conversion to the final units
and method are required
examples:
- value: 0.05 ug C/g dry soil
see_also:
- MIXS:0000650
rank: 10
string_serialization: '{float} {unit}'
slot_group: MIxS Inspired
microbial_biomass_n:
description: The part of the organic matter in the soil that constitutes living
microorganisms smaller than 5-10 micrometer.
title: microbial biomass nitrogen
comments:
- If you provide this, correction factors used for conversion to the final units
and method are required
examples:
- value: 0.05 ug N/g dry soil
see_also:
- MIXS:0000650
rank: 12
string_serialization: '{float} {unit}'
slot_group: MIxS Inspired
non_microb_biomass:
description: Amount of biomass; should include the name for the part of biomass
measured, e.g.insect, plant, total. Can include multiple measurements separated
by ;
title: non-microbial biomass
examples:
- value: insect 0.23 ug; plant 1g
see_also:
- MIXS:0000174
- MIXS:0000650
rank: 8
string_serialization: '{text};{float} {unit}'
slot_group: MIxS Inspired
non_microb_biomass_method:
description: Reference or method used in determining biomass
title: non-microbial biomass method
comments:
- required if "non-microbial biomass" is provided
examples:
- value: https://doi.org/10.1038/s41467-021-26181-3
see_also:
- MIXS:0000650
rank: 9
string_serialization: '{PMID}|{DOI}|{URL}'
slot_group: MIxS Inspired
org_nitro_method:
description: Method used for obtaining organic nitrogen
title: organic nitrogen method
comments:
- required if "org_nitro" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(85)90144-0
see_also:
- MIXS:0000338
- MIXS:0000205
rank: 14
string_serialization: '{PMID}|{DOI}|{URL}'
slot_group: MIxS Inspired
other_treatment:
description: Other treatments applied to your samples that are not applicable
to the provided fields
title: other treatments
notes:
- Values entered here will be used to determine potential new slots.
comments:
- This is an open text field to provide any treatments that cannot be captured
in the provided slots.
see_also:
- MIXS:0000300
rank: 15
string_serialization: '{text}'
slot_group: MIxS Inspired
recommended: true
start_date_inc:
description: Date the incubation was started. Only relevant for incubation samples.
title: incubation start date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
date only
comments:
- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
are all acceptable.
examples:
- value: 2021-04-15, 2021-04 and 2021 are all acceptable.
see_also:
- MIXS:0000011
rank: 4
string_serialization: '{date, arbitrary precision}'
slot_group: MIxS Inspired
recommended: true
start_time_inc:
description: Time the incubation was started. Only relevant for incubation samples.
title: incubation start time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
see_also:
- MIXS:0000011
rank: 5
string_serialization: '{time, seconds optional}'
slot_group: MIxS Inspired
recommended: true