Class: Soil MIxS Inspired Mixin (SoilMixsInspiredMixin)

name: SoilMixsInspiredMixin
description: Mixin with SoilMixsInspired Terms
title: Soil MIxS Inspired Mixin
from_schema: https://example.com/nmdc_submission_schema
mixin: true
slots:
- 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
- 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
slot_usage:
  collection_date_inc:
    name: 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.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 2
    string_serialization: '{date, arbitrary precision}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  collection_time:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 1
    string_serialization: '{time, seconds optional}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
  collection_time_inc:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 3
    string_serialization: '{time, seconds optional}'
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
  experimental_factor_other:
    name: 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'
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000008
    - MIXS:0000300
    rank: 7
    string_serialization: '{text}'
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  filter_method:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000765
    rank: 6
    string_serialization: '{text}'
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  isotope_exposure:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000751
    rank: 16
    string_serialization: '{termLabel} {[termID]}; {timestamp}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
  micro_biomass_c_meth:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000339
    rank: 1004
    string_serialization: '{PMID}|{DOI}|{URL}'
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  micro_biomass_n_meth:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000339
    rank: 1004
    string_serialization: '{PMID}|{DOI}|{URL}'
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
  microbial_biomass_c:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000650
    rank: 1004
    string_serialization: '{float} {unit}'
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
  microbial_biomass_n:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000650
    rank: 1004
    string_serialization: '{float} {unit}'
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
  non_microb_biomass:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000174
    - MIXS:0000650
    rank: 8
    string_serialization: '{text};{float} {unit}'
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  non_microb_biomass_method:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000650
    rank: 9
    string_serialization: '{PMID}|{DOI}|{URL}'
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
  org_nitro_method:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000338
    - MIXS:0000205
    rank: 14
    string_serialization: '{PMID}|{DOI}|{URL}'
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
  other_treatment:
    name: 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.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000300
    rank: 15
    string_serialization: '{text}'
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  start_date_inc:
    name: 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.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 4
    string_serialization: '{date, arbitrary precision}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  start_time_inc:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 5
    string_serialization: '{time, seconds optional}'
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$

name: SoilMixsInspiredMixin
description: Mixin with SoilMixsInspired Terms
title: Soil MIxS Inspired Mixin
from_schema: https://example.com/nmdc_submission_schema
mixin: true
slot_usage:
  collection_date_inc:
    name: 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.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 2
    string_serialization: '{date, arbitrary precision}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  collection_time:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 1
    string_serialization: '{time, seconds optional}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
  collection_time_inc:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 3
    string_serialization: '{time, seconds optional}'
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
  experimental_factor_other:
    name: 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'
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000008
    - MIXS:0000300
    rank: 7
    string_serialization: '{text}'
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  filter_method:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000765
    rank: 6
    string_serialization: '{text}'
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  isotope_exposure:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000751
    rank: 16
    string_serialization: '{termLabel} {[termID]}; {timestamp}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
  micro_biomass_c_meth:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000339
    rank: 1004
    string_serialization: '{PMID}|{DOI}|{URL}'
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  micro_biomass_n_meth:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000339
    rank: 1004
    string_serialization: '{PMID}|{DOI}|{URL}'
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
  microbial_biomass_c:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000650
    rank: 1004
    string_serialization: '{float} {unit}'
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
  microbial_biomass_n:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000650
    rank: 1004
    string_serialization: '{float} {unit}'
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
  non_microb_biomass:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000174
    - MIXS:0000650
    rank: 8
    string_serialization: '{text};{float} {unit}'
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  non_microb_biomass_method:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000650
    rank: 9
    string_serialization: '{PMID}|{DOI}|{URL}'
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
  org_nitro_method:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000338
    - MIXS:0000205
    rank: 14
    string_serialization: '{PMID}|{DOI}|{URL}'
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
  other_treatment:
    name: 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.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000300
    rank: 15
    string_serialization: '{text}'
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  start_date_inc:
    name: 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.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 4
    string_serialization: '{date, arbitrary precision}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  start_time_inc:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 5
    string_serialization: '{time, seconds optional}'
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
attributes:
  collection_date_inc:
    name: 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.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 2
    string_serialization: '{date, arbitrary precision}'
    alias: collection_date_inc
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  collection_time:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 1
    string_serialization: '{time, seconds optional}'
    alias: collection_time
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
  collection_time_inc:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 3
    string_serialization: '{time, seconds optional}'
    alias: collection_time_inc
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
  experimental_factor_other:
    name: 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'
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000008
    - MIXS:0000300
    rank: 7
    string_serialization: '{text}'
    alias: experimental_factor_other
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  filter_method:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000765
    rank: 6
    string_serialization: '{text}'
    alias: filter_method
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  isotope_exposure:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000751
    rank: 16
    string_serialization: '{termLabel} {[termID]}; {timestamp}'
    alias: isotope_exposure
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
  micro_biomass_c_meth:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000339
    rank: 1004
    string_serialization: '{PMID}|{DOI}|{URL}'
    alias: micro_biomass_c_meth
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  micro_biomass_n_meth:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000339
    rank: 1004
    string_serialization: '{PMID}|{DOI}|{URL}'
    alias: micro_biomass_n_meth
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
  microbial_biomass_c:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000650
    rank: 1004
    string_serialization: '{float} {unit}'
    alias: microbial_biomass_c
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
  microbial_biomass_n:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000650
    rank: 1004
    string_serialization: '{float} {unit}'
    alias: microbial_biomass_n
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
  non_microb_biomass:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000174
    - MIXS:0000650
    rank: 8
    string_serialization: '{text};{float} {unit}'
    alias: non_microb_biomass
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  non_microb_biomass_method:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000650
    rank: 9
    string_serialization: '{PMID}|{DOI}|{URL}'
    alias: non_microb_biomass_method
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
  org_nitro_method:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000338
    - MIXS:0000205
    rank: 14
    string_serialization: '{PMID}|{DOI}|{URL}'
    alias: org_nitro_method
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
  other_treatment:
    name: 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.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000300
    rank: 15
    string_serialization: '{text}'
    alias: other_treatment
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  start_date_inc:
    name: 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.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 4
    string_serialization: '{date, arbitrary precision}'
    alias: start_date_inc
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  start_time_inc:
    name: 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
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 5
    string_serialization: '{time, seconds optional}'
    alias: start_time_inc
    owner: SoilMixsInspiredMixin
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$