Class: Soil (SoilInterface)

name: SoilInterface
annotations:
  excel_worksheet_name:
    tag: excel_worksheet_name
    value: soil
description: soil dh_interface
title: Soil
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
- SampIdNewTermsMixin
- SoilMixsInspiredMixin
slots:
- agrochem_addition
- air_temp_regm
- al_sat
- al_sat_meth
- ammonium_nitrogen
- annual_precpt
- annual_temp
- biotic_regm
- biotic_relationship
- bulk_elect_conductivity
- carb_nitro_ratio
- chem_administration
- climate_environment
- collection_date
- collection_date_inc
- collection_time
- collection_time_inc
- crop_rotation
- cur_land_use
- cur_vegetation
- cur_vegetation_meth
- depth
- drainage_class
- ecosystem
- ecosystem_category
- ecosystem_subtype
- ecosystem_type
- elev
- env_broad_scale
- env_local_scale
- env_medium
- experimental_factor
- experimental_factor_other
- extreme_event
- fao_class
- filter_method
- fire
- flooding
- gaseous_environment
- geo_loc_name
- growth_facil
- heavy_metals
- heavy_metals_meth
- horizon_meth
- humidity_regm
- infiltrations
- isotope_exposure
- lat_lon
- lbc_thirty
- lbceq
- light_regm
- link_addit_analys
- link_class_info
- link_climate_info
- local_class
- local_class_meth
- manganese
- micro_biomass_c_meth
- micro_biomass_c_meth
- micro_biomass_meth
- micro_biomass_n_meth
- micro_biomass_n_meth
- microbial_biomass
- microbial_biomass_c
- microbial_biomass_c
- microbial_biomass_n
- microbial_biomass_n
- misc_param
- nitrate_nitrogen
- nitrite_nitrogen
- non_microb_biomass
- non_microb_biomass_method
- org_matter
- org_nitro
- org_nitro_method
- other_treatment
- oxy_stat_samp
- ph
- ph_meth
- phosphate
- prev_land_use_meth
- previous_land_use
- profile_position
- salinity
- salinity_meth
- samp_collec_device
- samp_collec_method
- samp_mat_process
- samp_size
- samp_store_temp
- sample_link
- season_precpt
- season_temp
- sieving
- size_frac_low
- size_frac_up
- slope_aspect
- slope_gradient
- soil_horizon
- soil_text_measure
- soil_texture_meth
- soil_type
- soil_type_meth
- specific_ecosystem
- start_date_inc
- start_time_inc
- store_cond
- temp
- tillage
- tot_carb
- tot_nitro_cont_meth
- tot_nitro_content
- tot_org_c_meth
- tot_org_carb
- tot_phosp
- water_cont_soil_meth
- water_content
- watering_regm
- zinc
slot_usage:
  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
      occurrence:
        tag: occurrence
        value: m
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/agrochemical additions
    rank: 2
    is_a: core field
    string_serialization: '{text};{float} {unit};{timestamp}'
    slot_uri: MIXS:0000639
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: .*
  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
      occurrence:
        tag: occurrence
        value: m
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - air temperature regimen
    rank: 16
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000551
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  al_sat:
    name: al_sat
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: percentage
      occurrence:
        tag: occurrence
        value: '1'
    description: The relative abundance of aluminum in the sample
    title: aluminum saturation/ extreme unusual properties
    todos:
    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will
      validate?
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
      I would argue this isn't an extreme unusual property. It's just a biogeochemical
      measurement.
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
      I would argue this isn't an extreme unusual property. It's just a biogeochemical
      measurement.
    notes:
    - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like
      all cations, aluminum held by the cation exchange complex is in equilibrium
      with aluminum in the soil solution.
    examples:
    - value: '0.27'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - extreme_unusual_properties/Al saturation
    rank: 3
    is_a: core field
    slot_uri: MIXS:0000607
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  al_sat_meth:
    name: al_sat_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or URL
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining Aluminum saturation
    title: aluminum saturation method/ extreme unusual properties
    todos:
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
    comments:
    - Required when aluminum saturation is provided.
    examples:
    - value: https://doi.org/10.1371/journal.pone.0176357
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - extreme_unusual_properties/Al saturation method
    rank: 4
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000324
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  ammonium_nitrogen:
    name: ammonium_nitrogen
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of ammonium nitrogen in the sample
    title: ammonium nitrogen
    examples:
    - value: 2.3 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - ammonium_nitrogen
    - NH4-N
    rank: 1005
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  annual_precpt:
    name: annual_precpt
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millimeter
      occurrence:
        tag: occurrence
        value: '1'
    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
    todos:
    - This is no longer matching the listed IRI from GSC, added example. When NMDC
      has its own slots, map this to the MIxS slot
    examples:
    - value: 8.94 inch
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean annual precipitation
    rank: 5
    is_a: core field
    slot_uri: MIXS:0000644
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  annual_temp:
    name: annual_temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: '1'
    description: Mean annual temperature
    title: mean annual temperature
    examples:
    - value: 12.5 degree Celsius
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean annual temperature
    rank: 6
    is_a: core field
    slot_uri: MIXS:0000642
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  biotic_regm:
    name: biotic_regm
    annotations:
      expected_value:
        tag: expected_value
        value: free text
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - biotic regimen
    rank: 13
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001038
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  biotic_relationship:
    name: biotic_relationship
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - observed biotic relationship
    rank: 22
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000028
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: biotic_relationship_enum
    multivalued: false
  bulk_elect_conductivity:
    name: bulk_elect_conductivity
    description: Electrical conductivity is a measure of the ability to carry electric
      current, which is mostly dictated by the chemistry of and amount of water.
    title: bulk electrical conductivity
    comments:
    - Provide the value output of the field instrument.
    examples:
    - value: 0.017 mS/cm
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1008
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  carb_nitro_ratio:
    name: carb_nitro_ratio
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    description: Ratio of amount or concentrations of carbon to nitrogen
    title: carbon/nitrogen ratio
    examples:
    - value: '0.417361111'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - carbon/nitrogen ratio
    rank: 44
    is_a: core field
    slot_uri: MIXS:0000310
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: float
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  chem_administration:
    name: chem_administration
    annotations:
      expected_value:
        tag: expected_value
        value: CHEBI;timestamp
      occurrence:
        tag: occurrence
        value: m
    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];2018-05-11|agar [CHEBI:2509];2018-05-22
    - value: agar [CHEBI:2509];2018-05
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chemical administration
    rank: 17
    is_a: core field
    string_serialization: '{termLabel} {[termID]};{timestamp}'
    slot_uri: MIXS:0000751
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_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)?)?)?)?$
  climate_environment:
    name: climate_environment
    annotations:
      expected_value:
        tag: expected_value
        value: climate name;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    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
    todos:
    - description says "can include multiple climates" but multivalued is set to false
    - add examples, i need to see some examples to add correctly formatted example.
    - description says "can include multiple climates" but multivalued is set to false
    - add examples, i need to see some examples to add correctly formatted example.
    examples:
    - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - climate environment
    rank: 19
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001040
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  collection_date:
    name: collection_date
    annotations:
      expected_value:
        tag: expected_value
        value: date and time
    description: The date of sampling
    title: collection date
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only
    - Use modified term (amended definition)
    examples:
    - value: '2021-04-15'
    - value: 2021-04
    - value: '2021'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - collection date
    rank: 3
    is_a: environment field
    string_serialization: '{date, arbitrary precision}'
    slot_uri: MIXS:0000011
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  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?$)):([0-5]\d)(:([0-5]\d))?$
  crop_rotation:
    name: crop_rotation
    annotations:
      expected_value:
        tag: expected_value
        value: crop rotation status;schedule
      occurrence:
        tag: occurrence
        value: '1'
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/crop rotation
    rank: 7
    is_a: core field
    string_serialization: '{boolean};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000318
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  cur_land_use:
    name: cur_land_use
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Present state of sample site
    title: current land use
    examples:
    - value: conifers
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - current land use
    rank: 8
    is_a: core field
    slot_uri: MIXS:0001080
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: cur_land_use_enum
    multivalued: false
  cur_vegetation:
    name: cur_vegetation
    annotations:
      expected_value:
        tag: expected_value
        value: current vegetation type
      occurrence:
        tag: occurrence
        value: '1'
    description: Vegetation classification from one or more standard classification
      systems, or agricultural crop
    title: current vegetation
    todos:
    - Recommend changing this from text value to some king of ontology?
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - Recommend changing this from text value to some kind of ontology?
    comments:
    - Values provided here can be specific species of vegetation or vegetation regions
    - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region
    examples:
    - value: deciduous forest
    - value: forest
    - value: Bauhinia variegata
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - current vegetation
    rank: 9
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000312
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  cur_vegetation_meth:
    name: cur_vegetation_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in vegetation classification
    title: current vegetation method
    todos:
    - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find
      out how they accomplish this if provided.
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find
      out how they accomplish this if provided.
    comments:
    - Required when current vegetation is provided.
    examples:
    - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - current vegetation method
    rank: 10
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000314
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  depth:
    name: depth
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: The vertical distance below local surface, e.g. 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, meters
    notes:
    - Use modified term
    comments:
    - All depths must be reported in meters. Provide the numerical portion only.
    examples:
    - value: 0 - 0.1
    - value: '1'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - depth
    rank: 9
    is_a: environment field
    string_serialization: '{float}-{float}'
    slot_uri: MIXS:0000018
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\s*-\s*[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$
  drainage_class:
    name: drainage_class
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Drainage classification from a standard system such as the USDA system
    title: drainage classification
    examples:
    - value: well
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - drainage classification
    rank: 11
    is_a: core field
    slot_uri: MIXS:0001085
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: drainage_class_enum
    multivalued: false
  ecosystem:
    name: ecosystem
    description: An ecosystem is a combination of a physical environment (abiotic
      factors) and all the organisms (biotic factors) that interact with this environment.
      Ecosystem is in position 1/5 in a GOLD path.
    comments:
    - The abiotic factors play a profound role on the type and composition of organisms
      in a given environment. The GOLD Ecosystem at the top of the five-level classification
      system is aimed at capturing the broader environment from which an organism
      or environmental sample is collected. The three broad groups under Ecosystem
      are Environmental, Host-associated, and Engineered. They represent samples collected
      from a natural environment or from another organism or from engineered environments
      like bioreactors respectively.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 9
    is_a: gold_path_field
    owner: Biosample
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemForSoilEnum
    recommended: true
  ecosystem_category:
    name: ecosystem_category
    description: Ecosystem categories represent divisions within the ecosystem based
      on specific characteristics of the environment from where an organism or sample
      is isolated. Ecosystem category is in position 2/5 in a GOLD path.
    comments:
    - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.
      Ecosystem categories for Host-associated samples can be individual hosts or
      phyla and for engineered samples it may be manipulated environments like bioreactors,
      solid waste etc.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 10
    is_a: gold_path_field
    owner: Biosample
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemCategoryForSoilEnum
    recommended: true
  ecosystem_subtype:
    name: ecosystem_subtype
    description: Ecosystem subtypes represent further subdivision of Ecosystem types
      into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD
      path.
    comments:
    - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided
      (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in
      the Ecosystem subtype category.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 12
    is_a: gold_path_field
    owner: Biosample
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemSubtypeForSoilEnum
    recommended: true
  ecosystem_type:
    name: ecosystem_type
    description: Ecosystem types represent things having common characteristics within
      the Ecosystem Category. These common characteristics based grouping is still
      broad but specific to the characteristics of a given environment. Ecosystem
      type is in position 3/5 in a GOLD path.
    comments:
    - The Aquatic ecosystem category (for example) may have ecosystem types like Marine
      or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor
      air as different Ecosystem Types. In the case of Host-associated samples, ecosystem
      type can represent Respiratory system, Digestive system, Roots etc.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 11
    is_a: gold_path_field
    owner: Biosample
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemTypeForSoilEnum
    recommended: true
  elev:
    name: elev
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    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, meters
    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: '225'
    - value: '0'
    - value: '1250'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - elevation
    rank: 6
    is_a: environment field
    slot_uri: MIXS:0000093
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: float
    required: true
    multivalued: false
  env_broad_scale:
    name: env_broad_scale
    annotations:
      expected_value:
        tag: expected_value
        value: The major environment type(s) where the sample was collected. Recommend
          subclasses of biome [ENVO:00000428]. Multiple terms can be separated by
          one or more pipes.
      tooltip:
        tag: tooltip
        value: The biome or major environmental system where the sample or specimen
          originated. Choose values from subclasses of the 'biome' class [ENVO:00000428]
          in the Environment Ontology (ENVO). For host-associated or plant-associated
          samples, use terms from the UBERON or Plant Ontology to describe the broad
          anatomical or morphological context
    description: 'In this field, report which major environmental system your sample
      or specimen came from. The systems identified should have a coarse spatial grain,
      to provide the general environmental context of where the sampling was done
      (e.g. were you in the desert or a rainforest?). We recommend using subclasses
      of ENVO''s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format
      (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel
      [termID]|termLabel [termID]. Example: Annotating a water sample from the photic
      zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome
      [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider:
      tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new
      terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html'
    title: broad-scale environmental context
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water
        sample from the photic zone in middle of the Atlantic Ocean
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - broad-scale environmental context
    rank: 6
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
    any_of:
    - range: EnvBroadScaleSoilEnum
    - range: string
  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.
      tooltip:
        tag: tooltip
        value: The specific environmental entities or features near the sample or
          specimen that significantly influence its characteristics or composition.
          These entities are typically smaller in scale than the broad environmental
          context. Values for this field should be countable, material nouns and must
          be chosen from subclasses of BFO:0000040 (material entity) that appear in
          the Environment Ontology (ENVO). For host-associated or plant-associated
          samples, use terms from the UBERON or Plant Ontology to describe specific
          anatomical structures or plant parts.
    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
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: canopy [ENVO:00000047]
    - value: herb and fern layer [ENVO:01000337]
    - value: litter layer [ENVO:01000338]
    - value: understory [01000335]
    - value: shrub layer [ENVO:01000336]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - local environmental context
    rank: 7
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000013
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
    any_of:
    - range: EnvLocalScaleSoilEnum
    - range: string
  env_medium:
    name: env_medium
    annotations:
      expected_value:
        tag: expected_value
        value: The material displaced by the entity at time of sampling. Recommend
          subclasses of environmental material [ENVO:00010483].
      tooltip:
        tag: tooltip
        value: The predominant environmental material or substrate that directly surrounds
          or hosts the sample or specimen at the time of sampling. Choose values from
          subclasses of the 'environmental material' class [ENVO:00010483] in the
          Environment Ontology (ENVO). Values for this field should be measurable
          or mass material nouns, representing continuous environmental materials.
          For host-associated or plant-associated samples, use terms from the UBERON
          or Plant Ontology to indicate a tissue, organ, or plant structure
    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
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: soil [ENVO:00001998]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - environmental medium
    rank: 8
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000014
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
    any_of:
    - range: EnvMediumSoilEnum
    - range: string
  experimental_factor:
    name: experimental_factor
    annotations:
      expected_value:
        tag: expected_value
        value: text or EFO and/or OBI
    description: Experimental factors are essentially the variable aspects of an experiment
      design which 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). For
      a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;
      for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
    title: experimental factor
    examples:
    - value: time series design [EFO:0001779]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - experimental factor
    rank: 12
    is_a: investigation field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000008
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  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
  extreme_event:
    name: extreme_event
    annotations:
      expected_value:
        tag: expected_value
        value: date, string
    description: Unusual physical events that may have affected microbial populations
    title: history/extreme events
    todos:
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    examples:
    - value: 1980-05-18, volcanic eruption
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/extreme events
    rank: 13
    is_a: core field
    slot_uri: MIXS:0000320
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  fao_class:
    name: fao_class
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil_taxonomic/FAO classification
    rank: 14
    is_a: core field
    slot_uri: MIXS:0001083
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: fao_class_enum
    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
  fire:
    name: fire
    annotations:
      expected_value:
        tag: expected_value
        value: date string
    description: Historical and/or physical evidence of fire
    title: history/fire
    todos:
    - is "to" acceptable? Is there a better way to request that be written?
    - is "to" acceptable? Is there a better way to request that be written?
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/fire
    rank: 15
    is_a: core field
    slot_uri: MIXS:0001086
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    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:
    name: flooding
    annotations:
      expected_value:
        tag: expected_value
        value: date string
    description: Historical and/or physical evidence of flooding
    title: history/flooding
    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?
    - is "to" acceptable? Is there a better way to request that be written?
    - What about if the "day" isn't known? Is this ok?
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/flooding
    rank: 16
    is_a: core field
    slot_uri: MIXS:0000319
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  gaseous_environment:
    name: gaseous_environment
    annotations:
      expected_value:
        tag: expected_value
        value: gaseous compound name;gaseous compound amount;treatment interval and
          duration
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: m
    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
    todos:
    - would like to see usage examples for this slot. Requiring micromole/L seems
      too limiting and doesn't match expected_value value
    - did I do this right? keep the example that's provided and add another? so as
      to not override
    - would like to see usage examples for this slot. Requiring micromole/L seems
      too limiting and doesn't match expected_value value
    - did I do this right? keep the example that's provided and add another? so as
      to not override
    examples:
    - value: CO2; 500ppm above ambient; constant
    - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gaseous environment
    rank: 20
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000558
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  geo_loc_name:
    name: geo_loc_name
    annotations:
      expected_value:
        tag: expected_value
        value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location
          name'
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name.
    title: geographic location (country and/or sea,region)
    examples:
    - value: 'USA: Maryland, Bethesda'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - geographic location (country and/or sea,region)
    rank: 4
    is_a: environment field
    string_serialization: '{text}: {text}, {text}'
    slot_uri: MIXS:0000010
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  growth_facil:
    name: growth_facil
    annotations:
      expected_value:
        tag: expected_value
        value: free text or CO
      occurrence:
        tag: occurrence
        value: '1'
    description: 'Type of facility/location where the sample was harvested; controlled
      vocabulary: growth chamber, open top chamber, glasshouse, experimental garden,
      field.'
    title: growth facility
    notes:
    - 'Removed from description: Alternatively use Crop Ontology (CO) terms'
    examples:
    - value: Growth chamber [CO_715:0000189]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - growth facility
    rank: 1
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001043
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: GrowthFacilEnum
    required: true
    multivalued: false
  heavy_metals:
    name: heavy_metals
    annotations:
      expected_value:
        tag: expected_value
        value: heavy metal name;measurement value unit
      preferred_unit:
        tag: preferred_unit
        value: microgram per gram
      occurrence:
        tag: occurrence
        value: m
    description: Heavy metals present in the sample and their concentrations.
    title: heavy metals/ extreme unusual properties
    todos:
    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will
      validate?
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
      I would argue this isn't an extreme unusual property. It's just a biogeochemical
      measurement.
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
      I would argue this isn't an extreme unusual property. It's just a biogeochemical
      measurement.
    notes:
    - Changed to multi-valued. In MIxS, you add another column to denote multiple
      heavy metals. We don't have that ability in the submission portal.
    comments:
    - For multiple heavy metals and concentrations, separate by ;
    examples:
    - value: mercury 0.09 micrograms per gram
    - value: mercury 0.09 ug/g; chromium 0.03 ug/g
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - extreme_unusual_properties/heavy metals
    rank: 17
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000652
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      [^;\t\r\x0A]+)$
  heavy_metals_meth:
    name: heavy_metals_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining heavy metals
    title: heavy metals method/ extreme unusual properties
    todos:
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    comments:
    - Required when heavy metals are provided
    - If different methods are used for multiple metals, indicate the metal and method.
      Separate metals by ;
    examples:
    - value: https://doi.org/10.3390/ijms9040434
    - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - extreme_unusual_properties/heavy metals method
    rank: 18
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000343
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  horizon_meth:
    name: horizon_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining the horizon
    title: soil horizon method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil horizon method
    rank: 19
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000321
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  humidity_regm:
    name: humidity_regm
    annotations:
      expected_value:
        tag: expected_value
        value: humidity value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram per cubic meter
      occurrence:
        tag: occurrence
        value: m
    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/nmdc/nmdc
    aliases:
    - humidity regimen
    rank: 21
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000568
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  infiltrations:
    name: infiltrations
    description: The amount of time it takes to complete each infiltration activity
    examples:
    - value: 00:01:32;00:00:53
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1
    aliases:
    - infiltration_1
    - infiltration_2
    rank: 1009
    list_elements_ordered: true
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^(?:(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9])(?:;(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9])*$
  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)?)?)?)?$
  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)
    notes:
    - This is currently a required field but it's not clear if this should be required
      for human hosts
    examples:
    - value: 50.586825 6.408977
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - geographic location (latitude and longitude)
    rank: 5
    is_a: environment field
    string_serialization: '{lat lon}'
    slot_uri: MIXS:0000009
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$
  lbc_thirty:
    name: lbc_thirty
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: ppm CaCO3/pH
      occurrence:
        tag: occurrence
        value: '1'
    description: lime buffer capacity, determined after 30 minute incubation
    title: lime buffer capacity (at 30 minutes)
    comments:
    - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by
      one pH unit
    examples:
    - value: 543 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    - https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF
    aliases:
    - lbc_thirty
    - lbc30
    - lime buffer capacity (at 30 minutes)
    rank: 1001
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  lbceq:
    name: lbceq
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: ppm CaCO3/pH
      occurrence:
        tag: occurrence
        value: '1'
    description: lime buffer capacity, determined at equilibrium after 5 day incubation
    title: lime buffer capacity (after 5 day incubation)
    comments:
    - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by
      one pH unit
    examples:
    - value: 1575 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - lbceq
    - lime buffer capacity (at 5-day equilibrium)
    rank: 1002
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about treatment(s) involving exposure to light, including
      both light intensity and quality.
    title: light regimen
    examples:
    - value: incandescant light;10 lux;450 nanometer
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - light regimen
    rank: 24
    is_a: core field
    string_serialization: '{text};{float} {unit};{float} {unit}'
    slot_uri: MIXS:0000569
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      \S+$
  link_addit_analys:
    name: link_addit_analys
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Link to additional analysis results performed on the sample
    title: links to additional analysis
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - links to additional analysis
    rank: 56
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000340
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  link_class_info:
    name: link_class_info
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Link to digitized soil maps or other soil classification information
    title: link to classification information
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - link to classification information
    rank: 20
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000329
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  link_climate_info:
    name: link_climate_info
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Link to climate resource
    title: link to climate information
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - link to climate information
    rank: 21
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000328
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  local_class:
    name: local_class
    annotations:
      expected_value:
        tag: expected_value
        value: local classification name
      occurrence:
        tag: occurrence
        value: '1'
    description: Soil classification based on local soil classification system
    title: soil_taxonomic/local classification
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil_taxonomic/local classification
    rank: 22
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000330
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  local_class_meth:
    name: local_class_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining the local soil classification
    title: soil_taxonomic/local classification method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil_taxonomic/local classification method
    rank: 24
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000331
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  manganese:
    name: manganese
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg (ppm)
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of manganese in the sample
    title: manganese
    examples:
    - value: 24.7 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - manganese
    rank: 1003
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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_meth:
    name: micro_biomass_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining microbial biomass
    title: microbial biomass method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - microbial biomass method
    rank: 43
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000339
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    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:
    name: microbial_biomass
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: ton, kilogram, gram per kilogram soil
      occurrence:
        tag: occurrence
        value: '1'
    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
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - microbial biomass
    rank: 42
    is_a: core field
    slot_uri: MIXS:0000650
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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+$
  misc_param:
    name: misc_param
    annotations:
      expected_value:
        tag: expected_value
        value: parameter name;measurement value
      occurrence:
        tag: occurrence
        value: m
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    examples:
    - value: Bicarbonate ion concentration;2075 micromole per kilogram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - miscellaneous parameter
    rank: 23
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      [^;\t\r\x0A]+)$
  nitrate_nitrogen:
    name: nitrate_nitrogen
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of nitrate nitrogen in the sample
    title: nitrate_nitrogen
    comments:
    - often below some specified limit of detection
    examples:
    - value: 0.29 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - nitrate_nitrogen
    - NO3-N
    rank: 1006
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  nitrite_nitrogen:
    name: nitrite_nitrogen
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of nitrite nitrogen in the sample
    title: nitrite_nitrogen
    examples:
    - value: 1.2 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - nitrite_nitrogen
    - NO2-N
    rank: 1007
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[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_matter:
    name: org_matter
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of organic matter
    title: organic matter
    examples:
    - value: 1.75 milligram per cubic meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organic matter
    rank: 45
    is_a: core field
    slot_uri: MIXS:0000204
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  org_nitro:
    name: org_nitro
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of organic nitrogen
    title: organic nitrogen
    examples:
    - value: 4 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organic nitrogen
    rank: 46
    is_a: core field
    slot_uri: MIXS:0000205
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
  oxy_stat_samp:
    name: oxy_stat_samp
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Oxygenation status of sample
    title: oxygenation status of sample
    examples:
    - value: aerobic
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - oxygenation status of sample
    rank: 25
    is_a: core field
    slot_uri: MIXS:0000753
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: OxyStatSampEnum
    multivalued: false
  ph:
    name: ph
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    description: pH measurement of the sample, or liquid portion of sample, or aqueous
      phase of the fluid
    title: pH
    notes:
    - Use modified term
    examples:
    - value: '7.2'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pH
    rank: 27
    is_a: core field
    string_serialization: '{float}'
    slot_uri: MIXS:0001001
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: float
    recommended: true
    multivalued: false
    minimum_value: 0
    maximum_value: 14
  ph_meth:
    name: ph_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining ph
    title: pH method
    comments:
    - This can include a link to the instrument used or a citation for the method.
    examples:
    - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB
    - value: https://doi.org/10.2136/sssabookser5.3.c16
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pH method
    rank: 41
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0001106
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  phosphate:
    name: phosphate
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of phosphate
    title: phosphate
    examples:
    - value: 0.7 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - phosphate
    rank: 53
    is_a: core field
    slot_uri: MIXS:0000505
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  prev_land_use_meth:
    name: prev_land_use_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining previous land use and dates
    title: history/previous land use method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/previous land use method
    rank: 26
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000316
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  previous_land_use:
    name: previous_land_use
    annotations:
      expected_value:
        tag: expected_value
        value: land use name;date
      occurrence:
        tag: occurrence
        value: '1'
    description: Previous land use and dates
    title: history/previous land use
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/previous land use
    rank: 27
    is_a: core field
    string_serialization: '{text};{timestamp}'
    slot_uri: MIXS:0000315
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^\S+.*\S+;([\+-]?\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)?)?)?)?$
  profile_position:
    name: profile_position
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - profile position
    rank: 28
    is_a: core field
    slot_uri: MIXS:0001084
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: profile_position_enum
    multivalued: false
  salinity:
    name: salinity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: practical salinity unit, percentage
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - salinity
    rank: 54
    is_a: core field
    slot_uri: MIXS:0000183
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  salinity_meth:
    name: salinity_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining salinity
    title: salinity method
    examples:
    - value: https://doi.org/10.1007/978-1-61779-986-0_28
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - salinity method
    rank: 55
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000341
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  samp_collec_device:
    name: samp_collec_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
    comments:
    - Report dimensions and details when applicable
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample collection device
    rank: 14
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000002
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  samp_collec_method:
    name: samp_collec_method
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url , or text
    description: The method employed for collecting the sample.
    title: sample collection method
    comments:
    - This can be a citation or description
    examples:
    - value: swabbing
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample collection method
    rank: 15
    is_a: nucleic acid sequence source field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001225
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
  samp_mat_process:
    name: samp_mat_process
    annotations:
      expected_value:
        tag: expected_value
        value: text
    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
    - value: storing samples in ethanol
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample material processing
    rank: 12
    is_a: nucleic acid sequence source field
    string_serialization: '{text}'
    slot_uri: MIXS:0000016
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
  samp_size:
    name: samp_size
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millliter, gram, milligram, liter
    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
      sample collected.
    title: amount or size of sample collected
    comments:
    - This refers to the TOTAL amount of sample collected from the experiment. NOT
      the amount sent to each institution or collected for a specific analysis.
    examples:
    - value: 5 grams
    - value: 10 mL
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - amount or size of sample collected
    rank: 18
    is_a: nucleic acid sequence source field
    string_serialization: '{float} {unit}'
    slot_uri: MIXS:0000001
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
  samp_store_temp:
    name: samp_store_temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: '1'
    description: Temperature at which the sample was stored (degrees are assumed)
    title: sample storage temperature
    examples:
    - value: -80 Celsius
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample storage temperature
    rank: 7
    is_a: core field
    slot_uri: MIXS:0000110
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  sample_link:
    name: sample_link
    description: A unique identifier to assign parent-child, subsample, or sibling
      samples. This is relevant when a sample or other material was used to generate
      the new sample.
    title: sample linkage
    notes:
    - 'also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) >
      1 and "placeholder" in slot_usage.keys():AttributeError: ''list'' object has
      no attribute ''keys'''
    comments:
    - 'This field allows multiple entries separated by ; (Examples: Soil collected
      from the field will link with the soil used in an incubation. The soil a plant
      was grown in links to the plant sample. An original culture sample was transferred
      to a new vial and generated a new sample)'
    examples:
    - value: IGSN:DSJ0284
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 5
    string_serialization: '{text}:{text}'
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    - SampIdNewTermsMixin
    slot_group: sample_id_section
    range: string
    recommended: true
    multivalued: false
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'
  season_precpt:
    name: season_precpt
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millimeter
      occurrence:
        tag: occurrence
        value: '1'
    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: average seasonal precipitation
    todos:
    - check validation & examples. always mm? so value only? Or value + unit
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - check validation & examples. always mm? so value only? Or value + unit
    notes:
    - mean and average are the same thing, but it seems like bad practice to not be
      consistent. Changed mean to average
    - mean and average are the same thing, but it seems like bad practice to not be
      consistent. Changed mean to average
    comments:
    - Seasons are defined as spring (March, April, May), summer (June, July, August),
      autumn (September, October, November) and winter (December, January, February).
    examples:
    - value: 0.4 inch
    - value: 10.16 mm
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean seasonal precipitation
    rank: 29
    is_a: core field
    slot_uri: MIXS:0000645
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  season_temp:
    name: season_temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: '1'
    description: Mean seasonal temperature
    title: mean seasonal temperature
    examples:
    - value: 18 degree Celsius
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean seasonal temperature
    rank: 30
    is_a: core field
    slot_uri: MIXS:0000643
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  sieving:
    name: sieving
    annotations:
      expected_value:
        tag: expected_value
        value: design name and/or size;amount
      occurrence:
        tag: occurrence
        value: '1'
    description: Collection design of pooled samples and/or sieve size and amount
      of sample sieved
    title: composite design/sieving
    todos:
    - check validation and examples
    - check validation and examples
    comments:
    - Describe how samples were composited or sieved.
    - Use 'sample link' to indicate which samples were combined.
    examples:
    - value: combined 2 cores
    - value: 4mm sieved
    - value: 4 mm sieved and homogenized
    - value: 50 g
    - value: 5 cores
    - value: 2 mm sieved
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - composite design/sieving
    rank: 8
    is_a: core field
    string_serialization: '{{text}|{float} {unit}};{float} {unit}'
    slot_uri: MIXS:0000322
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  size_frac_low:
    name: size_frac_low
    annotations:
      expected_value:
        tag: expected_value
        value: value
      preferred_unit:
        tag: preferred_unit
        value: micrometer
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - size-fraction lower threshold
    rank: 10
    is_a: core field
    slot_uri: MIXS:0000735
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: false
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  size_frac_up:
    name: size_frac_up
    annotations:
      expected_value:
        tag: expected_value
        value: value
      preferred_unit:
        tag: preferred_unit
        value: micrometer
      occurrence:
        tag: occurrence
        value: '1'
    description: Refers to the mesh/pore size 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/nmdc/nmdc
    aliases:
    - size-fraction upper threshold
    rank: 11
    is_a: core field
    slot_uri: MIXS:0000736
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: false
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  slope_aspect:
    name: slope_aspect
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree
      occurrence:
        tag: occurrence
        value: '1'
    description: The direction a slope faces. While looking down a slope use a compass
      to record the direction you are facing (direction or degrees). - This measure
      provides an indication of sun and wind exposure that will influence soil temperature
      and evapotranspiration.
    title: slope aspect
    todos:
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    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.
    examples:
    - value: '35'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - slope aspect
    rank: 1
    is_a: core field
    slot_uri: MIXS:0000647
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  slope_gradient:
    name: slope_gradient
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: percentage
      occurrence:
        tag: occurrence
        value: '1'
    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
    todos:
    - Slope is a percent. How does the validation work? Check to correct examples
    - Slope is a percent. How does the validation work? Check to correct examples
    examples:
    - value: 10%
    - value: 10 %
    - value: '0.1'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - slope gradient
    rank: 31
    is_a: core field
    slot_uri: MIXS:0000646
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  soil_horizon:
    name: soil_horizon
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - soil horizon
    rank: 32
    is_a: core field
    slot_uri: MIXS:0001082
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: soil_horizon_enum
    multivalued: false
  soil_text_measure:
    name: soil_text_measure
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    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 measurement
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil texture measurement
    rank: 33
    is_a: core field
    slot_uri: MIXS:0000335
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  soil_texture_meth:
    name: soil_texture_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining soil texture
    title: soil texture method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil texture method
    rank: 34
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000336
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  soil_type:
    name: soil_type
    annotations:
      expected_value:
        tag: expected_value
        value: ENVO_00001998
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - soil type
    rank: 35
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000332
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  soil_type_meth:
    name: soil_type_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining soil series name or other
      lower-level classification
    title: soil type method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil type method
    rank: 36
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000334
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  specific_ecosystem:
    name: specific_ecosystem
    description: Specific ecosystems represent specific features of the environment
      like aphotic zone in an ocean or gastric mucosa within a host digestive system.
      Specific ecosystem is in position 5/5 in a GOLD path.
    comments:
    - Specific ecosystems help to define samples based on very specific characteristics
      of an environment under the five-level classification system.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 13
    is_a: gold_path_field
    owner: Biosample
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: SpecificEcosystemForSoilEnum
    recommended: true
  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?$)):([0-5]\d)(:([0-5]\d))?$
  store_cond:
    name: store_cond
    annotations:
      expected_value:
        tag: expected_value
        value: storage condition type;duration
      occurrence:
        tag: occurrence
        value: '1'
    description: Explain how the soil sample is stored (fresh/frozen/other).
    title: storage conditions
    examples:
    - value: -20 degree Celsius freezer;P2Y10D
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - storage conditions
    rank: 2
    is_a: core field
    string_serialization: '{text};{duration}'
    slot_uri: MIXS:0000327
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_modified_section
    range: StoreCondEnum
    required: true
    multivalued: false
  temp:
    name: temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - temperature
    rank: 37
    is_a: environment field
    slot_uri: MIXS:0000113
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tillage:
    name: tillage
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: m
    description: Note method(s) used for tilling
    title: history/tillage
    examples:
    - value: chisel
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/tillage
    rank: 38
    is_a: core field
    slot_uri: MIXS:0001081
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: tillage_enum
    multivalued: true
  tot_carb:
    name: tot_carb
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Total carbon content
    title: total carbon
    todos:
    - is this inorganic and organic? both? could use some clarification.
    - ug/L doesn't seem like the right units. Should check this slots usage in databases
      and re-evaluate. I couldn't find any references that provided this data in this
      format
    - is this inorganic and organic? both? could use some clarification.
    - ug/L doesn't seem like the right units. Should check this slots usage in databases
      and re-evaluate. I couldn't find any references that provided this data in this
      format
    examples:
    - value: 1 ug/L
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total carbon
    rank: 47
    is_a: core field
    slot_uri: MIXS:0000525
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tot_nitro_cont_meth:
    name: tot_nitro_cont_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining the total nitrogen
    title: total nitrogen content method
    examples:
    - value: https://doi.org/10.2134/agronmonogr9.2.c32
    - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total nitrogen content method
    rank: 49
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000338
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  tot_nitro_content:
    name: tot_nitro_content
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, micromole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Total nitrogen content of the sample
    title: total nitrogen content
    examples:
    - value: 5 mg N/ L
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total nitrogen content
    rank: 48
    is_a: core field
    slot_uri: MIXS:0000530
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tot_org_c_meth:
    name: tot_org_c_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining total organic carbon
    title: total organic carbon method
    examples:
    - value: https://doi.org/10.1080/07352680902776556
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total organic carbon method
    rank: 51
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000337
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  tot_org_carb:
    name: tot_org_carb
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram Carbon per kilogram sample material
      occurrence:
        tag: occurrence
        value: '1'
    description: 'Definition for soil: total organic carbon content of the soil, definition
      otherwise: total organic carbon content'
    title: total organic carbon
    todos:
    - check description. How are they different?
    - check description. How are they different?
    examples:
    - value: 5 mg N/ L
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total organic carbon
    rank: 50
    is_a: core field
    slot_uri: MIXS:0000533
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tot_phosp:
    name: tot_phosp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter, milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - total phosphorus
    rank: 52
    is_a: core field
    slot_uri: MIXS:0000117
    owner: Biosample
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  water_cont_soil_meth:
    name: water_cont_soil_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining the water content of soil
    title: water content method
    todos:
    - Why is it soil water content method in the name but not the title? Is this slot
      used in other samples?
    - Soil water content can be measure MANY ways and often, multiple ways are used
      in one experiment (gravimetric water content and water holding capacity and
      water filled pore space, to name a few).
    - Should this be multi valued? How to we manage and validate this?
    - Why is it soil water content method in the name but not the title? Is this slot
      used in other samples?
    - Soil water content can be measure MANY ways and often, multiple ways are used
      in one experiment (gravimetric water content and water holding capacity and
      water filled pore space, to name a few).
    - Should this be multi valued? How to we manage and validate this?
    comments:
    - Required if providing water content
    examples:
    - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503
    - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - water content method
    rank: 40
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000323
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  water_content:
    name: water_content
    annotations:
      expected_value:
        tag: expected_value
        value: string
      preferred_unit:
        tag: preferred_unit
        value: gram per gram or cubic centimeter per cubic centimeter
    description: Water content measurement
    title: water content
    todos:
    - value in preferred unit is too limiting. need to change this
    - check and correct validation so examples are accepted
    - how to manage multiple water content methods?
    examples:
    - value: 0.75 g water/g dry soil
    - value: 75% water holding capacity
    - value: 1.1 g fresh weight/ dry weight
    - value: 10% water filled pore space
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - water content
    rank: 39
    is_a: core field
    string_serialization: '{float or pct} {unit}'
    slot_uri: MIXS:0000185
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?%? \S.+$
  watering_regm:
    name: watering_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: milliliter, liter
      occurrence:
        tag: occurrence
        value: m
    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
    - value: 75% water holding capacity; constant
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - watering regimen
    rank: 25
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000591
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  zinc:
    name: zinc
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg (ppm)
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of zinc in the sample
    title: zinc
    examples:
    - value: 2.5 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - zinc
    rank: 1004
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  organism_count:
    name: organism_count
    range: string
    multivalued: false
    pattern: ^(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+.*\S+;(qPCR|ATP|MPN|other)\|)*(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      \S+.*\S+;(qPCR|ATP|MPN|other))$

name: SoilInterface
annotations:
  excel_worksheet_name:
    tag: excel_worksheet_name
    value: soil
description: soil dh_interface
title: Soil
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
- SampIdNewTermsMixin
- SoilMixsInspiredMixin
slot_usage:
  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
      occurrence:
        tag: occurrence
        value: m
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/agrochemical additions
    rank: 2
    is_a: core field
    string_serialization: '{text};{float} {unit};{timestamp}'
    slot_uri: MIXS:0000639
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: .*
  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
      occurrence:
        tag: occurrence
        value: m
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - air temperature regimen
    rank: 16
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000551
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  al_sat:
    name: al_sat
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: percentage
      occurrence:
        tag: occurrence
        value: '1'
    description: The relative abundance of aluminum in the sample
    title: aluminum saturation/ extreme unusual properties
    todos:
    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will
      validate?
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
      I would argue this isn't an extreme unusual property. It's just a biogeochemical
      measurement.
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
      I would argue this isn't an extreme unusual property. It's just a biogeochemical
      measurement.
    notes:
    - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like
      all cations, aluminum held by the cation exchange complex is in equilibrium
      with aluminum in the soil solution.
    examples:
    - value: '0.27'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - extreme_unusual_properties/Al saturation
    rank: 3
    is_a: core field
    slot_uri: MIXS:0000607
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  al_sat_meth:
    name: al_sat_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or URL
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining Aluminum saturation
    title: aluminum saturation method/ extreme unusual properties
    todos:
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
    comments:
    - Required when aluminum saturation is provided.
    examples:
    - value: https://doi.org/10.1371/journal.pone.0176357
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - extreme_unusual_properties/Al saturation method
    rank: 4
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000324
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  ammonium_nitrogen:
    name: ammonium_nitrogen
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of ammonium nitrogen in the sample
    title: ammonium nitrogen
    examples:
    - value: 2.3 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - ammonium_nitrogen
    - NH4-N
    rank: 1005
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  annual_precpt:
    name: annual_precpt
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millimeter
      occurrence:
        tag: occurrence
        value: '1'
    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
    todos:
    - This is no longer matching the listed IRI from GSC, added example. When NMDC
      has its own slots, map this to the MIxS slot
    examples:
    - value: 8.94 inch
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean annual precipitation
    rank: 5
    is_a: core field
    slot_uri: MIXS:0000644
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  annual_temp:
    name: annual_temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: '1'
    description: Mean annual temperature
    title: mean annual temperature
    examples:
    - value: 12.5 degree Celsius
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean annual temperature
    rank: 6
    is_a: core field
    slot_uri: MIXS:0000642
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  biotic_regm:
    name: biotic_regm
    annotations:
      expected_value:
        tag: expected_value
        value: free text
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - biotic regimen
    rank: 13
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001038
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  biotic_relationship:
    name: biotic_relationship
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - observed biotic relationship
    rank: 22
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000028
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: biotic_relationship_enum
    multivalued: false
  bulk_elect_conductivity:
    name: bulk_elect_conductivity
    description: Electrical conductivity is a measure of the ability to carry electric
      current, which is mostly dictated by the chemistry of and amount of water.
    title: bulk electrical conductivity
    comments:
    - Provide the value output of the field instrument.
    examples:
    - value: 0.017 mS/cm
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1008
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  carb_nitro_ratio:
    name: carb_nitro_ratio
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    description: Ratio of amount or concentrations of carbon to nitrogen
    title: carbon/nitrogen ratio
    examples:
    - value: '0.417361111'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - carbon/nitrogen ratio
    rank: 44
    is_a: core field
    slot_uri: MIXS:0000310
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: float
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  chem_administration:
    name: chem_administration
    annotations:
      expected_value:
        tag: expected_value
        value: CHEBI;timestamp
      occurrence:
        tag: occurrence
        value: m
    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];2018-05-11|agar [CHEBI:2509];2018-05-22
    - value: agar [CHEBI:2509];2018-05
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chemical administration
    rank: 17
    is_a: core field
    string_serialization: '{termLabel} {[termID]};{timestamp}'
    slot_uri: MIXS:0000751
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_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)?)?)?)?$
  climate_environment:
    name: climate_environment
    annotations:
      expected_value:
        tag: expected_value
        value: climate name;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    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
    todos:
    - description says "can include multiple climates" but multivalued is set to false
    - add examples, i need to see some examples to add correctly formatted example.
    - description says "can include multiple climates" but multivalued is set to false
    - add examples, i need to see some examples to add correctly formatted example.
    examples:
    - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - climate environment
    rank: 19
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001040
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  collection_date:
    name: collection_date
    annotations:
      expected_value:
        tag: expected_value
        value: date and time
    description: The date of sampling
    title: collection date
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only
    - Use modified term (amended definition)
    examples:
    - value: '2021-04-15'
    - value: 2021-04
    - value: '2021'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - collection date
    rank: 3
    is_a: environment field
    string_serialization: '{date, arbitrary precision}'
    slot_uri: MIXS:0000011
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  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?$)):([0-5]\d)(:([0-5]\d))?$
  crop_rotation:
    name: crop_rotation
    annotations:
      expected_value:
        tag: expected_value
        value: crop rotation status;schedule
      occurrence:
        tag: occurrence
        value: '1'
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/crop rotation
    rank: 7
    is_a: core field
    string_serialization: '{boolean};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000318
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  cur_land_use:
    name: cur_land_use
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Present state of sample site
    title: current land use
    examples:
    - value: conifers
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - current land use
    rank: 8
    is_a: core field
    slot_uri: MIXS:0001080
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: cur_land_use_enum
    multivalued: false
  cur_vegetation:
    name: cur_vegetation
    annotations:
      expected_value:
        tag: expected_value
        value: current vegetation type
      occurrence:
        tag: occurrence
        value: '1'
    description: Vegetation classification from one or more standard classification
      systems, or agricultural crop
    title: current vegetation
    todos:
    - Recommend changing this from text value to some king of ontology?
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - Recommend changing this from text value to some kind of ontology?
    comments:
    - Values provided here can be specific species of vegetation or vegetation regions
    - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region
    examples:
    - value: deciduous forest
    - value: forest
    - value: Bauhinia variegata
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - current vegetation
    rank: 9
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000312
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  cur_vegetation_meth:
    name: cur_vegetation_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in vegetation classification
    title: current vegetation method
    todos:
    - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find
      out how they accomplish this if provided.
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find
      out how they accomplish this if provided.
    comments:
    - Required when current vegetation is provided.
    examples:
    - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - current vegetation method
    rank: 10
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000314
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  depth:
    name: depth
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: The vertical distance below local surface, e.g. 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, meters
    notes:
    - Use modified term
    comments:
    - All depths must be reported in meters. Provide the numerical portion only.
    examples:
    - value: 0 - 0.1
    - value: '1'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - depth
    rank: 9
    is_a: environment field
    string_serialization: '{float}-{float}'
    slot_uri: MIXS:0000018
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\s*-\s*[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$
  drainage_class:
    name: drainage_class
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Drainage classification from a standard system such as the USDA system
    title: drainage classification
    examples:
    - value: well
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - drainage classification
    rank: 11
    is_a: core field
    slot_uri: MIXS:0001085
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: drainage_class_enum
    multivalued: false
  ecosystem:
    name: ecosystem
    description: An ecosystem is a combination of a physical environment (abiotic
      factors) and all the organisms (biotic factors) that interact with this environment.
      Ecosystem is in position 1/5 in a GOLD path.
    comments:
    - The abiotic factors play a profound role on the type and composition of organisms
      in a given environment. The GOLD Ecosystem at the top of the five-level classification
      system is aimed at capturing the broader environment from which an organism
      or environmental sample is collected. The three broad groups under Ecosystem
      are Environmental, Host-associated, and Engineered. They represent samples collected
      from a natural environment or from another organism or from engineered environments
      like bioreactors respectively.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 9
    is_a: gold_path_field
    owner: Biosample
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemForSoilEnum
    recommended: true
  ecosystem_category:
    name: ecosystem_category
    description: Ecosystem categories represent divisions within the ecosystem based
      on specific characteristics of the environment from where an organism or sample
      is isolated. Ecosystem category is in position 2/5 in a GOLD path.
    comments:
    - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.
      Ecosystem categories for Host-associated samples can be individual hosts or
      phyla and for engineered samples it may be manipulated environments like bioreactors,
      solid waste etc.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 10
    is_a: gold_path_field
    owner: Biosample
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemCategoryForSoilEnum
    recommended: true
  ecosystem_subtype:
    name: ecosystem_subtype
    description: Ecosystem subtypes represent further subdivision of Ecosystem types
      into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD
      path.
    comments:
    - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided
      (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in
      the Ecosystem subtype category.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 12
    is_a: gold_path_field
    owner: Biosample
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemSubtypeForSoilEnum
    recommended: true
  ecosystem_type:
    name: ecosystem_type
    description: Ecosystem types represent things having common characteristics within
      the Ecosystem Category. These common characteristics based grouping is still
      broad but specific to the characteristics of a given environment. Ecosystem
      type is in position 3/5 in a GOLD path.
    comments:
    - The Aquatic ecosystem category (for example) may have ecosystem types like Marine
      or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor
      air as different Ecosystem Types. In the case of Host-associated samples, ecosystem
      type can represent Respiratory system, Digestive system, Roots etc.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 11
    is_a: gold_path_field
    owner: Biosample
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemTypeForSoilEnum
    recommended: true
  elev:
    name: elev
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    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, meters
    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: '225'
    - value: '0'
    - value: '1250'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - elevation
    rank: 6
    is_a: environment field
    slot_uri: MIXS:0000093
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: float
    required: true
    multivalued: false
  env_broad_scale:
    name: env_broad_scale
    annotations:
      expected_value:
        tag: expected_value
        value: The major environment type(s) where the sample was collected. Recommend
          subclasses of biome [ENVO:00000428]. Multiple terms can be separated by
          one or more pipes.
      tooltip:
        tag: tooltip
        value: The biome or major environmental system where the sample or specimen
          originated. Choose values from subclasses of the 'biome' class [ENVO:00000428]
          in the Environment Ontology (ENVO). For host-associated or plant-associated
          samples, use terms from the UBERON or Plant Ontology to describe the broad
          anatomical or morphological context
    description: 'In this field, report which major environmental system your sample
      or specimen came from. The systems identified should have a coarse spatial grain,
      to provide the general environmental context of where the sampling was done
      (e.g. were you in the desert or a rainforest?). We recommend using subclasses
      of ENVO''s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format
      (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel
      [termID]|termLabel [termID]. Example: Annotating a water sample from the photic
      zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome
      [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider:
      tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new
      terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html'
    title: broad-scale environmental context
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water
        sample from the photic zone in middle of the Atlantic Ocean
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - broad-scale environmental context
    rank: 6
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
    any_of:
    - range: EnvBroadScaleSoilEnum
    - range: string
  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.
      tooltip:
        tag: tooltip
        value: The specific environmental entities or features near the sample or
          specimen that significantly influence its characteristics or composition.
          These entities are typically smaller in scale than the broad environmental
          context. Values for this field should be countable, material nouns and must
          be chosen from subclasses of BFO:0000040 (material entity) that appear in
          the Environment Ontology (ENVO). For host-associated or plant-associated
          samples, use terms from the UBERON or Plant Ontology to describe specific
          anatomical structures or plant parts.
    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
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: canopy [ENVO:00000047]
    - value: herb and fern layer [ENVO:01000337]
    - value: litter layer [ENVO:01000338]
    - value: understory [01000335]
    - value: shrub layer [ENVO:01000336]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - local environmental context
    rank: 7
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000013
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
    any_of:
    - range: EnvLocalScaleSoilEnum
    - range: string
  env_medium:
    name: env_medium
    annotations:
      expected_value:
        tag: expected_value
        value: The material displaced by the entity at time of sampling. Recommend
          subclasses of environmental material [ENVO:00010483].
      tooltip:
        tag: tooltip
        value: The predominant environmental material or substrate that directly surrounds
          or hosts the sample or specimen at the time of sampling. Choose values from
          subclasses of the 'environmental material' class [ENVO:00010483] in the
          Environment Ontology (ENVO). Values for this field should be measurable
          or mass material nouns, representing continuous environmental materials.
          For host-associated or plant-associated samples, use terms from the UBERON
          or Plant Ontology to indicate a tissue, organ, or plant structure
    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
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: soil [ENVO:00001998]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - environmental medium
    rank: 8
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000014
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
    any_of:
    - range: EnvMediumSoilEnum
    - range: string
  experimental_factor:
    name: experimental_factor
    annotations:
      expected_value:
        tag: expected_value
        value: text or EFO and/or OBI
    description: Experimental factors are essentially the variable aspects of an experiment
      design which 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). For
      a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;
      for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
    title: experimental factor
    examples:
    - value: time series design [EFO:0001779]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - experimental factor
    rank: 12
    is_a: investigation field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000008
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  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
  extreme_event:
    name: extreme_event
    annotations:
      expected_value:
        tag: expected_value
        value: date, string
    description: Unusual physical events that may have affected microbial populations
    title: history/extreme events
    todos:
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    examples:
    - value: 1980-05-18, volcanic eruption
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/extreme events
    rank: 13
    is_a: core field
    slot_uri: MIXS:0000320
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  fao_class:
    name: fao_class
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil_taxonomic/FAO classification
    rank: 14
    is_a: core field
    slot_uri: MIXS:0001083
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: fao_class_enum
    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
  fire:
    name: fire
    annotations:
      expected_value:
        tag: expected_value
        value: date string
    description: Historical and/or physical evidence of fire
    title: history/fire
    todos:
    - is "to" acceptable? Is there a better way to request that be written?
    - is "to" acceptable? Is there a better way to request that be written?
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/fire
    rank: 15
    is_a: core field
    slot_uri: MIXS:0001086
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    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:
    name: flooding
    annotations:
      expected_value:
        tag: expected_value
        value: date string
    description: Historical and/or physical evidence of flooding
    title: history/flooding
    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?
    - is "to" acceptable? Is there a better way to request that be written?
    - What about if the "day" isn't known? Is this ok?
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/flooding
    rank: 16
    is_a: core field
    slot_uri: MIXS:0000319
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  gaseous_environment:
    name: gaseous_environment
    annotations:
      expected_value:
        tag: expected_value
        value: gaseous compound name;gaseous compound amount;treatment interval and
          duration
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: m
    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
    todos:
    - would like to see usage examples for this slot. Requiring micromole/L seems
      too limiting and doesn't match expected_value value
    - did I do this right? keep the example that's provided and add another? so as
      to not override
    - would like to see usage examples for this slot. Requiring micromole/L seems
      too limiting and doesn't match expected_value value
    - did I do this right? keep the example that's provided and add another? so as
      to not override
    examples:
    - value: CO2; 500ppm above ambient; constant
    - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gaseous environment
    rank: 20
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000558
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  geo_loc_name:
    name: geo_loc_name
    annotations:
      expected_value:
        tag: expected_value
        value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location
          name'
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name.
    title: geographic location (country and/or sea,region)
    examples:
    - value: 'USA: Maryland, Bethesda'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - geographic location (country and/or sea,region)
    rank: 4
    is_a: environment field
    string_serialization: '{text}: {text}, {text}'
    slot_uri: MIXS:0000010
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  growth_facil:
    name: growth_facil
    annotations:
      expected_value:
        tag: expected_value
        value: free text or CO
      occurrence:
        tag: occurrence
        value: '1'
    description: 'Type of facility/location where the sample was harvested; controlled
      vocabulary: growth chamber, open top chamber, glasshouse, experimental garden,
      field.'
    title: growth facility
    notes:
    - 'Removed from description: Alternatively use Crop Ontology (CO) terms'
    examples:
    - value: Growth chamber [CO_715:0000189]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - growth facility
    rank: 1
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001043
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: GrowthFacilEnum
    required: true
    multivalued: false
  heavy_metals:
    name: heavy_metals
    annotations:
      expected_value:
        tag: expected_value
        value: heavy metal name;measurement value unit
      preferred_unit:
        tag: preferred_unit
        value: microgram per gram
      occurrence:
        tag: occurrence
        value: m
    description: Heavy metals present in the sample and their concentrations.
    title: heavy metals/ extreme unusual properties
    todos:
    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will
      validate?
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
      I would argue this isn't an extreme unusual property. It's just a biogeochemical
      measurement.
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
      I would argue this isn't an extreme unusual property. It's just a biogeochemical
      measurement.
    notes:
    - Changed to multi-valued. In MIxS, you add another column to denote multiple
      heavy metals. We don't have that ability in the submission portal.
    comments:
    - For multiple heavy metals and concentrations, separate by ;
    examples:
    - value: mercury 0.09 micrograms per gram
    - value: mercury 0.09 ug/g; chromium 0.03 ug/g
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - extreme_unusual_properties/heavy metals
    rank: 17
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000652
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      [^;\t\r\x0A]+)$
  heavy_metals_meth:
    name: heavy_metals_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining heavy metals
    title: heavy metals method/ extreme unusual properties
    todos:
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    comments:
    - Required when heavy metals are provided
    - If different methods are used for multiple metals, indicate the metal and method.
      Separate metals by ;
    examples:
    - value: https://doi.org/10.3390/ijms9040434
    - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - extreme_unusual_properties/heavy metals method
    rank: 18
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000343
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  horizon_meth:
    name: horizon_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining the horizon
    title: soil horizon method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil horizon method
    rank: 19
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000321
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  humidity_regm:
    name: humidity_regm
    annotations:
      expected_value:
        tag: expected_value
        value: humidity value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram per cubic meter
      occurrence:
        tag: occurrence
        value: m
    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/nmdc/nmdc
    aliases:
    - humidity regimen
    rank: 21
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000568
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  infiltrations:
    name: infiltrations
    description: The amount of time it takes to complete each infiltration activity
    examples:
    - value: 00:01:32;00:00:53
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1
    aliases:
    - infiltration_1
    - infiltration_2
    rank: 1009
    list_elements_ordered: true
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^(?:(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9])(?:;(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9])*$
  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)?)?)?)?$
  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)
    notes:
    - This is currently a required field but it's not clear if this should be required
      for human hosts
    examples:
    - value: 50.586825 6.408977
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - geographic location (latitude and longitude)
    rank: 5
    is_a: environment field
    string_serialization: '{lat lon}'
    slot_uri: MIXS:0000009
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$
  lbc_thirty:
    name: lbc_thirty
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: ppm CaCO3/pH
      occurrence:
        tag: occurrence
        value: '1'
    description: lime buffer capacity, determined after 30 minute incubation
    title: lime buffer capacity (at 30 minutes)
    comments:
    - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by
      one pH unit
    examples:
    - value: 543 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    - https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF
    aliases:
    - lbc_thirty
    - lbc30
    - lime buffer capacity (at 30 minutes)
    rank: 1001
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  lbceq:
    name: lbceq
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: ppm CaCO3/pH
      occurrence:
        tag: occurrence
        value: '1'
    description: lime buffer capacity, determined at equilibrium after 5 day incubation
    title: lime buffer capacity (after 5 day incubation)
    comments:
    - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by
      one pH unit
    examples:
    - value: 1575 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - lbceq
    - lime buffer capacity (at 5-day equilibrium)
    rank: 1002
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about treatment(s) involving exposure to light, including
      both light intensity and quality.
    title: light regimen
    examples:
    - value: incandescant light;10 lux;450 nanometer
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - light regimen
    rank: 24
    is_a: core field
    string_serialization: '{text};{float} {unit};{float} {unit}'
    slot_uri: MIXS:0000569
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      \S+$
  link_addit_analys:
    name: link_addit_analys
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Link to additional analysis results performed on the sample
    title: links to additional analysis
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - links to additional analysis
    rank: 56
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000340
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  link_class_info:
    name: link_class_info
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Link to digitized soil maps or other soil classification information
    title: link to classification information
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - link to classification information
    rank: 20
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000329
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  link_climate_info:
    name: link_climate_info
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Link to climate resource
    title: link to climate information
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - link to climate information
    rank: 21
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000328
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  local_class:
    name: local_class
    annotations:
      expected_value:
        tag: expected_value
        value: local classification name
      occurrence:
        tag: occurrence
        value: '1'
    description: Soil classification based on local soil classification system
    title: soil_taxonomic/local classification
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil_taxonomic/local classification
    rank: 22
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000330
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  local_class_meth:
    name: local_class_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining the local soil classification
    title: soil_taxonomic/local classification method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil_taxonomic/local classification method
    rank: 24
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000331
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  manganese:
    name: manganese
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg (ppm)
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of manganese in the sample
    title: manganese
    examples:
    - value: 24.7 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - manganese
    rank: 1003
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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_meth:
    name: micro_biomass_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining microbial biomass
    title: microbial biomass method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - microbial biomass method
    rank: 43
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000339
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    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:
    name: microbial_biomass
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: ton, kilogram, gram per kilogram soil
      occurrence:
        tag: occurrence
        value: '1'
    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
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - microbial biomass
    rank: 42
    is_a: core field
    slot_uri: MIXS:0000650
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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+$
  misc_param:
    name: misc_param
    annotations:
      expected_value:
        tag: expected_value
        value: parameter name;measurement value
      occurrence:
        tag: occurrence
        value: m
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    examples:
    - value: Bicarbonate ion concentration;2075 micromole per kilogram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - miscellaneous parameter
    rank: 23
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      [^;\t\r\x0A]+)$
  nitrate_nitrogen:
    name: nitrate_nitrogen
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of nitrate nitrogen in the sample
    title: nitrate_nitrogen
    comments:
    - often below some specified limit of detection
    examples:
    - value: 0.29 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - nitrate_nitrogen
    - NO3-N
    rank: 1006
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  nitrite_nitrogen:
    name: nitrite_nitrogen
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of nitrite nitrogen in the sample
    title: nitrite_nitrogen
    examples:
    - value: 1.2 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - nitrite_nitrogen
    - NO2-N
    rank: 1007
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[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_matter:
    name: org_matter
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of organic matter
    title: organic matter
    examples:
    - value: 1.75 milligram per cubic meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organic matter
    rank: 45
    is_a: core field
    slot_uri: MIXS:0000204
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  org_nitro:
    name: org_nitro
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of organic nitrogen
    title: organic nitrogen
    examples:
    - value: 4 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organic nitrogen
    rank: 46
    is_a: core field
    slot_uri: MIXS:0000205
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
  oxy_stat_samp:
    name: oxy_stat_samp
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Oxygenation status of sample
    title: oxygenation status of sample
    examples:
    - value: aerobic
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - oxygenation status of sample
    rank: 25
    is_a: core field
    slot_uri: MIXS:0000753
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: OxyStatSampEnum
    multivalued: false
  ph:
    name: ph
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    description: pH measurement of the sample, or liquid portion of sample, or aqueous
      phase of the fluid
    title: pH
    notes:
    - Use modified term
    examples:
    - value: '7.2'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pH
    rank: 27
    is_a: core field
    string_serialization: '{float}'
    slot_uri: MIXS:0001001
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: float
    recommended: true
    multivalued: false
    minimum_value: 0
    maximum_value: 14
  ph_meth:
    name: ph_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining ph
    title: pH method
    comments:
    - This can include a link to the instrument used or a citation for the method.
    examples:
    - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB
    - value: https://doi.org/10.2136/sssabookser5.3.c16
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pH method
    rank: 41
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0001106
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  phosphate:
    name: phosphate
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of phosphate
    title: phosphate
    examples:
    - value: 0.7 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - phosphate
    rank: 53
    is_a: core field
    slot_uri: MIXS:0000505
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  prev_land_use_meth:
    name: prev_land_use_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining previous land use and dates
    title: history/previous land use method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/previous land use method
    rank: 26
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000316
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  previous_land_use:
    name: previous_land_use
    annotations:
      expected_value:
        tag: expected_value
        value: land use name;date
      occurrence:
        tag: occurrence
        value: '1'
    description: Previous land use and dates
    title: history/previous land use
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/previous land use
    rank: 27
    is_a: core field
    string_serialization: '{text};{timestamp}'
    slot_uri: MIXS:0000315
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^\S+.*\S+;([\+-]?\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)?)?)?)?$
  profile_position:
    name: profile_position
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - profile position
    rank: 28
    is_a: core field
    slot_uri: MIXS:0001084
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: profile_position_enum
    multivalued: false
  salinity:
    name: salinity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: practical salinity unit, percentage
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - salinity
    rank: 54
    is_a: core field
    slot_uri: MIXS:0000183
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  salinity_meth:
    name: salinity_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining salinity
    title: salinity method
    examples:
    - value: https://doi.org/10.1007/978-1-61779-986-0_28
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - salinity method
    rank: 55
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000341
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  samp_collec_device:
    name: samp_collec_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
    comments:
    - Report dimensions and details when applicable
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample collection device
    rank: 14
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000002
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  samp_collec_method:
    name: samp_collec_method
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url , or text
    description: The method employed for collecting the sample.
    title: sample collection method
    comments:
    - This can be a citation or description
    examples:
    - value: swabbing
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample collection method
    rank: 15
    is_a: nucleic acid sequence source field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001225
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
  samp_mat_process:
    name: samp_mat_process
    annotations:
      expected_value:
        tag: expected_value
        value: text
    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
    - value: storing samples in ethanol
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample material processing
    rank: 12
    is_a: nucleic acid sequence source field
    string_serialization: '{text}'
    slot_uri: MIXS:0000016
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
  samp_size:
    name: samp_size
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millliter, gram, milligram, liter
    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
      sample collected.
    title: amount or size of sample collected
    comments:
    - This refers to the TOTAL amount of sample collected from the experiment. NOT
      the amount sent to each institution or collected for a specific analysis.
    examples:
    - value: 5 grams
    - value: 10 mL
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - amount or size of sample collected
    rank: 18
    is_a: nucleic acid sequence source field
    string_serialization: '{float} {unit}'
    slot_uri: MIXS:0000001
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
  samp_store_temp:
    name: samp_store_temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: '1'
    description: Temperature at which the sample was stored (degrees are assumed)
    title: sample storage temperature
    examples:
    - value: -80 Celsius
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample storage temperature
    rank: 7
    is_a: core field
    slot_uri: MIXS:0000110
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  sample_link:
    name: sample_link
    description: A unique identifier to assign parent-child, subsample, or sibling
      samples. This is relevant when a sample or other material was used to generate
      the new sample.
    title: sample linkage
    notes:
    - 'also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) >
      1 and "placeholder" in slot_usage.keys():AttributeError: ''list'' object has
      no attribute ''keys'''
    comments:
    - 'This field allows multiple entries separated by ; (Examples: Soil collected
      from the field will link with the soil used in an incubation. The soil a plant
      was grown in links to the plant sample. An original culture sample was transferred
      to a new vial and generated a new sample)'
    examples:
    - value: IGSN:DSJ0284
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 5
    string_serialization: '{text}:{text}'
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    - SampIdNewTermsMixin
    slot_group: sample_id_section
    range: string
    recommended: true
    multivalued: false
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'
  season_precpt:
    name: season_precpt
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millimeter
      occurrence:
        tag: occurrence
        value: '1'
    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: average seasonal precipitation
    todos:
    - check validation & examples. always mm? so value only? Or value + unit
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - check validation & examples. always mm? so value only? Or value + unit
    notes:
    - mean and average are the same thing, but it seems like bad practice to not be
      consistent. Changed mean to average
    - mean and average are the same thing, but it seems like bad practice to not be
      consistent. Changed mean to average
    comments:
    - Seasons are defined as spring (March, April, May), summer (June, July, August),
      autumn (September, October, November) and winter (December, January, February).
    examples:
    - value: 0.4 inch
    - value: 10.16 mm
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean seasonal precipitation
    rank: 29
    is_a: core field
    slot_uri: MIXS:0000645
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  season_temp:
    name: season_temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: '1'
    description: Mean seasonal temperature
    title: mean seasonal temperature
    examples:
    - value: 18 degree Celsius
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean seasonal temperature
    rank: 30
    is_a: core field
    slot_uri: MIXS:0000643
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  sieving:
    name: sieving
    annotations:
      expected_value:
        tag: expected_value
        value: design name and/or size;amount
      occurrence:
        tag: occurrence
        value: '1'
    description: Collection design of pooled samples and/or sieve size and amount
      of sample sieved
    title: composite design/sieving
    todos:
    - check validation and examples
    - check validation and examples
    comments:
    - Describe how samples were composited or sieved.
    - Use 'sample link' to indicate which samples were combined.
    examples:
    - value: combined 2 cores
    - value: 4mm sieved
    - value: 4 mm sieved and homogenized
    - value: 50 g
    - value: 5 cores
    - value: 2 mm sieved
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - composite design/sieving
    rank: 8
    is_a: core field
    string_serialization: '{{text}|{float} {unit}};{float} {unit}'
    slot_uri: MIXS:0000322
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  size_frac_low:
    name: size_frac_low
    annotations:
      expected_value:
        tag: expected_value
        value: value
      preferred_unit:
        tag: preferred_unit
        value: micrometer
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - size-fraction lower threshold
    rank: 10
    is_a: core field
    slot_uri: MIXS:0000735
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: false
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  size_frac_up:
    name: size_frac_up
    annotations:
      expected_value:
        tag: expected_value
        value: value
      preferred_unit:
        tag: preferred_unit
        value: micrometer
      occurrence:
        tag: occurrence
        value: '1'
    description: Refers to the mesh/pore size 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/nmdc/nmdc
    aliases:
    - size-fraction upper threshold
    rank: 11
    is_a: core field
    slot_uri: MIXS:0000736
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: false
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  slope_aspect:
    name: slope_aspect
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree
      occurrence:
        tag: occurrence
        value: '1'
    description: The direction a slope faces. While looking down a slope use a compass
      to record the direction you are facing (direction or degrees). - This measure
      provides an indication of sun and wind exposure that will influence soil temperature
      and evapotranspiration.
    title: slope aspect
    todos:
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    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.
    examples:
    - value: '35'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - slope aspect
    rank: 1
    is_a: core field
    slot_uri: MIXS:0000647
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  slope_gradient:
    name: slope_gradient
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: percentage
      occurrence:
        tag: occurrence
        value: '1'
    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
    todos:
    - Slope is a percent. How does the validation work? Check to correct examples
    - Slope is a percent. How does the validation work? Check to correct examples
    examples:
    - value: 10%
    - value: 10 %
    - value: '0.1'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - slope gradient
    rank: 31
    is_a: core field
    slot_uri: MIXS:0000646
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  soil_horizon:
    name: soil_horizon
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - soil horizon
    rank: 32
    is_a: core field
    slot_uri: MIXS:0001082
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: soil_horizon_enum
    multivalued: false
  soil_text_measure:
    name: soil_text_measure
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    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 measurement
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil texture measurement
    rank: 33
    is_a: core field
    slot_uri: MIXS:0000335
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  soil_texture_meth:
    name: soil_texture_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining soil texture
    title: soil texture method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil texture method
    rank: 34
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000336
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  soil_type:
    name: soil_type
    annotations:
      expected_value:
        tag: expected_value
        value: ENVO_00001998
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - soil type
    rank: 35
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000332
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  soil_type_meth:
    name: soil_type_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining soil series name or other
      lower-level classification
    title: soil type method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil type method
    rank: 36
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000334
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  specific_ecosystem:
    name: specific_ecosystem
    description: Specific ecosystems represent specific features of the environment
      like aphotic zone in an ocean or gastric mucosa within a host digestive system.
      Specific ecosystem is in position 5/5 in a GOLD path.
    comments:
    - Specific ecosystems help to define samples based on very specific characteristics
      of an environment under the five-level classification system.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 13
    is_a: gold_path_field
    owner: Biosample
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: SpecificEcosystemForSoilEnum
    recommended: true
  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?$)):([0-5]\d)(:([0-5]\d))?$
  store_cond:
    name: store_cond
    annotations:
      expected_value:
        tag: expected_value
        value: storage condition type;duration
      occurrence:
        tag: occurrence
        value: '1'
    description: Explain how the soil sample is stored (fresh/frozen/other).
    title: storage conditions
    examples:
    - value: -20 degree Celsius freezer;P2Y10D
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - storage conditions
    rank: 2
    is_a: core field
    string_serialization: '{text};{duration}'
    slot_uri: MIXS:0000327
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_modified_section
    range: StoreCondEnum
    required: true
    multivalued: false
  temp:
    name: temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - temperature
    rank: 37
    is_a: environment field
    slot_uri: MIXS:0000113
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tillage:
    name: tillage
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: m
    description: Note method(s) used for tilling
    title: history/tillage
    examples:
    - value: chisel
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/tillage
    rank: 38
    is_a: core field
    slot_uri: MIXS:0001081
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: tillage_enum
    multivalued: true
  tot_carb:
    name: tot_carb
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Total carbon content
    title: total carbon
    todos:
    - is this inorganic and organic? both? could use some clarification.
    - ug/L doesn't seem like the right units. Should check this slots usage in databases
      and re-evaluate. I couldn't find any references that provided this data in this
      format
    - is this inorganic and organic? both? could use some clarification.
    - ug/L doesn't seem like the right units. Should check this slots usage in databases
      and re-evaluate. I couldn't find any references that provided this data in this
      format
    examples:
    - value: 1 ug/L
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total carbon
    rank: 47
    is_a: core field
    slot_uri: MIXS:0000525
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tot_nitro_cont_meth:
    name: tot_nitro_cont_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining the total nitrogen
    title: total nitrogen content method
    examples:
    - value: https://doi.org/10.2134/agronmonogr9.2.c32
    - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total nitrogen content method
    rank: 49
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000338
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  tot_nitro_content:
    name: tot_nitro_content
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, micromole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Total nitrogen content of the sample
    title: total nitrogen content
    examples:
    - value: 5 mg N/ L
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total nitrogen content
    rank: 48
    is_a: core field
    slot_uri: MIXS:0000530
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tot_org_c_meth:
    name: tot_org_c_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining total organic carbon
    title: total organic carbon method
    examples:
    - value: https://doi.org/10.1080/07352680902776556
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total organic carbon method
    rank: 51
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000337
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  tot_org_carb:
    name: tot_org_carb
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram Carbon per kilogram sample material
      occurrence:
        tag: occurrence
        value: '1'
    description: 'Definition for soil: total organic carbon content of the soil, definition
      otherwise: total organic carbon content'
    title: total organic carbon
    todos:
    - check description. How are they different?
    - check description. How are they different?
    examples:
    - value: 5 mg N/ L
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total organic carbon
    rank: 50
    is_a: core field
    slot_uri: MIXS:0000533
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tot_phosp:
    name: tot_phosp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter, milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - total phosphorus
    rank: 52
    is_a: core field
    slot_uri: MIXS:0000117
    owner: Biosample
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  water_cont_soil_meth:
    name: water_cont_soil_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining the water content of soil
    title: water content method
    todos:
    - Why is it soil water content method in the name but not the title? Is this slot
      used in other samples?
    - Soil water content can be measure MANY ways and often, multiple ways are used
      in one experiment (gravimetric water content and water holding capacity and
      water filled pore space, to name a few).
    - Should this be multi valued? How to we manage and validate this?
    - Why is it soil water content method in the name but not the title? Is this slot
      used in other samples?
    - Soil water content can be measure MANY ways and often, multiple ways are used
      in one experiment (gravimetric water content and water holding capacity and
      water filled pore space, to name a few).
    - Should this be multi valued? How to we manage and validate this?
    comments:
    - Required if providing water content
    examples:
    - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503
    - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - water content method
    rank: 40
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000323
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  water_content:
    name: water_content
    annotations:
      expected_value:
        tag: expected_value
        value: string
      preferred_unit:
        tag: preferred_unit
        value: gram per gram or cubic centimeter per cubic centimeter
    description: Water content measurement
    title: water content
    todos:
    - value in preferred unit is too limiting. need to change this
    - check and correct validation so examples are accepted
    - how to manage multiple water content methods?
    examples:
    - value: 0.75 g water/g dry soil
    - value: 75% water holding capacity
    - value: 1.1 g fresh weight/ dry weight
    - value: 10% water filled pore space
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - water content
    rank: 39
    is_a: core field
    string_serialization: '{float or pct} {unit}'
    slot_uri: MIXS:0000185
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?%? \S.+$
  watering_regm:
    name: watering_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: milliliter, liter
      occurrence:
        tag: occurrence
        value: m
    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
    - value: 75% water holding capacity; constant
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - watering regimen
    rank: 25
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000591
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  zinc:
    name: zinc
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg (ppm)
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of zinc in the sample
    title: zinc
    examples:
    - value: 2.5 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - zinc
    rank: 1004
    owner: Biosample
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  organism_count:
    name: organism_count
    range: string
    multivalued: false
    pattern: ^(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+.*\S+;(qPCR|ATP|MPN|other)\|)*(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      \S+.*\S+;(qPCR|ATP|MPN|other))$
attributes:
  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
      occurrence:
        tag: occurrence
        value: m
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/agrochemical additions
    rank: 2
    is_a: core field
    string_serialization: '{text};{float} {unit};{timestamp}'
    slot_uri: MIXS:0000639
    alias: agrochem_addition
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: .*
  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
      occurrence:
        tag: occurrence
        value: m
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - air temperature regimen
    rank: 16
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000551
    alias: air_temp_regm
    owner: SoilInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  al_sat:
    name: al_sat
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: percentage
      occurrence:
        tag: occurrence
        value: '1'
    description: The relative abundance of aluminum in the sample
    title: aluminum saturation/ extreme unusual properties
    todos:
    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will
      validate?
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
      I would argue this isn't an extreme unusual property. It's just a biogeochemical
      measurement.
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
      I would argue this isn't an extreme unusual property. It's just a biogeochemical
      measurement.
    notes:
    - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like
      all cations, aluminum held by the cation exchange complex is in equilibrium
      with aluminum in the soil solution.
    examples:
    - value: '0.27'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - extreme_unusual_properties/Al saturation
    rank: 3
    is_a: core field
    slot_uri: MIXS:0000607
    alias: al_sat
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  al_sat_meth:
    name: al_sat_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or URL
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining Aluminum saturation
    title: aluminum saturation method/ extreme unusual properties
    todos:
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
    comments:
    - Required when aluminum saturation is provided.
    examples:
    - value: https://doi.org/10.1371/journal.pone.0176357
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - extreme_unusual_properties/Al saturation method
    rank: 4
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000324
    alias: al_sat_meth
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  ammonium_nitrogen:
    name: ammonium_nitrogen
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of ammonium nitrogen in the sample
    title: ammonium nitrogen
    examples:
    - value: 2.3 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - ammonium_nitrogen
    - NH4-N
    rank: 1005
    alias: ammonium_nitrogen
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  annual_precpt:
    name: annual_precpt
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millimeter
      occurrence:
        tag: occurrence
        value: '1'
    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
    todos:
    - This is no longer matching the listed IRI from GSC, added example. When NMDC
      has its own slots, map this to the MIxS slot
    examples:
    - value: 8.94 inch
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean annual precipitation
    rank: 5
    is_a: core field
    slot_uri: MIXS:0000644
    alias: annual_precpt
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  annual_temp:
    name: annual_temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: '1'
    description: Mean annual temperature
    title: mean annual temperature
    examples:
    - value: 12.5 degree Celsius
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean annual temperature
    rank: 6
    is_a: core field
    slot_uri: MIXS:0000642
    alias: annual_temp
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  biotic_regm:
    name: biotic_regm
    annotations:
      expected_value:
        tag: expected_value
        value: free text
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - biotic regimen
    rank: 13
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001038
    alias: biotic_regm
    owner: SoilInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  biotic_relationship:
    name: biotic_relationship
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - observed biotic relationship
    rank: 22
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000028
    alias: biotic_relationship
    owner: SoilInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: biotic_relationship_enum
    multivalued: false
  bulk_elect_conductivity:
    name: bulk_elect_conductivity
    description: Electrical conductivity is a measure of the ability to carry electric
      current, which is mostly dictated by the chemistry of and amount of water.
    title: bulk electrical conductivity
    comments:
    - Provide the value output of the field instrument.
    examples:
    - value: 0.017 mS/cm
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1008
    alias: bulk_elect_conductivity
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  carb_nitro_ratio:
    name: carb_nitro_ratio
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    description: Ratio of amount or concentrations of carbon to nitrogen
    title: carbon/nitrogen ratio
    examples:
    - value: '0.417361111'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - carbon/nitrogen ratio
    rank: 44
    is_a: core field
    slot_uri: MIXS:0000310
    alias: carb_nitro_ratio
    owner: SoilInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: float
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  chem_administration:
    name: chem_administration
    annotations:
      expected_value:
        tag: expected_value
        value: CHEBI;timestamp
      occurrence:
        tag: occurrence
        value: m
    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];2018-05-11|agar [CHEBI:2509];2018-05-22
    - value: agar [CHEBI:2509];2018-05
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chemical administration
    rank: 17
    is_a: core field
    string_serialization: '{termLabel} {[termID]};{timestamp}'
    slot_uri: MIXS:0000751
    alias: chem_administration
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_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)?)?)?)?$
  climate_environment:
    name: climate_environment
    annotations:
      expected_value:
        tag: expected_value
        value: climate name;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    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
    todos:
    - description says "can include multiple climates" but multivalued is set to false
    - add examples, i need to see some examples to add correctly formatted example.
    - description says "can include multiple climates" but multivalued is set to false
    - add examples, i need to see some examples to add correctly formatted example.
    examples:
    - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - climate environment
    rank: 19
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001040
    alias: climate_environment
    owner: SoilInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  collection_date:
    name: collection_date
    annotations:
      expected_value:
        tag: expected_value
        value: date and time
    description: The date of sampling
    title: collection date
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only
    - Use modified term (amended definition)
    examples:
    - value: '2021-04-15'
    - value: 2021-04
    - value: '2021'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - collection date
    rank: 3
    is_a: environment field
    string_serialization: '{date, arbitrary precision}'
    slot_uri: MIXS:0000011
    alias: collection_date
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  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: SoilInterface
    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: SoilInterface
    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: SoilInterface
    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?$)):([0-5]\d)(:([0-5]\d))?$
  crop_rotation:
    name: crop_rotation
    annotations:
      expected_value:
        tag: expected_value
        value: crop rotation status;schedule
      occurrence:
        tag: occurrence
        value: '1'
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/crop rotation
    rank: 7
    is_a: core field
    string_serialization: '{boolean};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000318
    alias: crop_rotation
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  cur_land_use:
    name: cur_land_use
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Present state of sample site
    title: current land use
    examples:
    - value: conifers
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - current land use
    rank: 8
    is_a: core field
    slot_uri: MIXS:0001080
    alias: cur_land_use
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: cur_land_use_enum
    multivalued: false
  cur_vegetation:
    name: cur_vegetation
    annotations:
      expected_value:
        tag: expected_value
        value: current vegetation type
      occurrence:
        tag: occurrence
        value: '1'
    description: Vegetation classification from one or more standard classification
      systems, or agricultural crop
    title: current vegetation
    todos:
    - Recommend changing this from text value to some king of ontology?
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - Recommend changing this from text value to some kind of ontology?
    comments:
    - Values provided here can be specific species of vegetation or vegetation regions
    - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region
    examples:
    - value: deciduous forest
    - value: forest
    - value: Bauhinia variegata
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - current vegetation
    rank: 9
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000312
    alias: cur_vegetation
    owner: SoilInterface
    domain_of:
    - FieldResearchSite
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  cur_vegetation_meth:
    name: cur_vegetation_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in vegetation classification
    title: current vegetation method
    todos:
    - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find
      out how they accomplish this if provided.
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find
      out how they accomplish this if provided.
    comments:
    - Required when current vegetation is provided.
    examples:
    - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - current vegetation method
    rank: 10
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000314
    alias: cur_vegetation_meth
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  depth:
    name: depth
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: The vertical distance below local surface, e.g. 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, meters
    notes:
    - Use modified term
    comments:
    - All depths must be reported in meters. Provide the numerical portion only.
    examples:
    - value: 0 - 0.1
    - value: '1'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - depth
    rank: 9
    is_a: environment field
    string_serialization: '{float}-{float}'
    slot_uri: MIXS:0000018
    alias: depth
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\s*-\s*[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$
  drainage_class:
    name: drainage_class
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Drainage classification from a standard system such as the USDA system
    title: drainage classification
    examples:
    - value: well
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - drainage classification
    rank: 11
    is_a: core field
    slot_uri: MIXS:0001085
    alias: drainage_class
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: drainage_class_enum
    multivalued: false
  ecosystem:
    name: ecosystem
    description: An ecosystem is a combination of a physical environment (abiotic
      factors) and all the organisms (biotic factors) that interact with this environment.
      Ecosystem is in position 1/5 in a GOLD path.
    comments:
    - The abiotic factors play a profound role on the type and composition of organisms
      in a given environment. The GOLD Ecosystem at the top of the five-level classification
      system is aimed at capturing the broader environment from which an organism
      or environmental sample is collected. The three broad groups under Ecosystem
      are Environmental, Host-associated, and Engineered. They represent samples collected
      from a natural environment or from another organism or from engineered environments
      like bioreactors respectively.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 9
    is_a: gold_path_field
    alias: ecosystem
    owner: SoilInterface
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemForSoilEnum
    recommended: true
  ecosystem_category:
    name: ecosystem_category
    description: Ecosystem categories represent divisions within the ecosystem based
      on specific characteristics of the environment from where an organism or sample
      is isolated. Ecosystem category is in position 2/5 in a GOLD path.
    comments:
    - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.
      Ecosystem categories for Host-associated samples can be individual hosts or
      phyla and for engineered samples it may be manipulated environments like bioreactors,
      solid waste etc.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 10
    is_a: gold_path_field
    alias: ecosystem_category
    owner: SoilInterface
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemCategoryForSoilEnum
    recommended: true
  ecosystem_subtype:
    name: ecosystem_subtype
    description: Ecosystem subtypes represent further subdivision of Ecosystem types
      into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD
      path.
    comments:
    - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided
      (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in
      the Ecosystem subtype category.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 12
    is_a: gold_path_field
    alias: ecosystem_subtype
    owner: SoilInterface
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemSubtypeForSoilEnum
    recommended: true
  ecosystem_type:
    name: ecosystem_type
    description: Ecosystem types represent things having common characteristics within
      the Ecosystem Category. These common characteristics based grouping is still
      broad but specific to the characteristics of a given environment. Ecosystem
      type is in position 3/5 in a GOLD path.
    comments:
    - The Aquatic ecosystem category (for example) may have ecosystem types like Marine
      or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor
      air as different Ecosystem Types. In the case of Host-associated samples, ecosystem
      type can represent Respiratory system, Digestive system, Roots etc.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 11
    is_a: gold_path_field
    alias: ecosystem_type
    owner: SoilInterface
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemTypeForSoilEnum
    recommended: true
  elev:
    name: elev
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    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, meters
    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: '225'
    - value: '0'
    - value: '1250'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - elevation
    rank: 6
    is_a: environment field
    slot_uri: MIXS:0000093
    alias: elev
    owner: SoilInterface
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: float
    required: true
    multivalued: false
  env_broad_scale:
    name: env_broad_scale
    annotations:
      expected_value:
        tag: expected_value
        value: The major environment type(s) where the sample was collected. Recommend
          subclasses of biome [ENVO:00000428]. Multiple terms can be separated by
          one or more pipes.
      tooltip:
        tag: tooltip
        value: The biome or major environmental system where the sample or specimen
          originated. Choose values from subclasses of the 'biome' class [ENVO:00000428]
          in the Environment Ontology (ENVO). For host-associated or plant-associated
          samples, use terms from the UBERON or Plant Ontology to describe the broad
          anatomical or morphological context
    description: 'In this field, report which major environmental system your sample
      or specimen came from. The systems identified should have a coarse spatial grain,
      to provide the general environmental context of where the sampling was done
      (e.g. were you in the desert or a rainforest?). We recommend using subclasses
      of ENVO''s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format
      (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel
      [termID]|termLabel [termID]. Example: Annotating a water sample from the photic
      zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome
      [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider:
      tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new
      terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html'
    title: broad-scale environmental context
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water
        sample from the photic zone in middle of the Atlantic Ocean
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - broad-scale environmental context
    rank: 6
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    alias: env_broad_scale
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
    any_of:
    - range: EnvBroadScaleSoilEnum
    - range: string
  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.
      tooltip:
        tag: tooltip
        value: The specific environmental entities or features near the sample or
          specimen that significantly influence its characteristics or composition.
          These entities are typically smaller in scale than the broad environmental
          context. Values for this field should be countable, material nouns and must
          be chosen from subclasses of BFO:0000040 (material entity) that appear in
          the Environment Ontology (ENVO). For host-associated or plant-associated
          samples, use terms from the UBERON or Plant Ontology to describe specific
          anatomical structures or plant parts.
    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
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: canopy [ENVO:00000047]
    - value: herb and fern layer [ENVO:01000337]
    - value: litter layer [ENVO:01000338]
    - value: understory [01000335]
    - value: shrub layer [ENVO:01000336]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - local environmental context
    rank: 7
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000013
    alias: env_local_scale
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
    any_of:
    - range: EnvLocalScaleSoilEnum
    - range: string
  env_medium:
    name: env_medium
    annotations:
      expected_value:
        tag: expected_value
        value: The material displaced by the entity at time of sampling. Recommend
          subclasses of environmental material [ENVO:00010483].
      tooltip:
        tag: tooltip
        value: The predominant environmental material or substrate that directly surrounds
          or hosts the sample or specimen at the time of sampling. Choose values from
          subclasses of the 'environmental material' class [ENVO:00010483] in the
          Environment Ontology (ENVO). Values for this field should be measurable
          or mass material nouns, representing continuous environmental materials.
          For host-associated or plant-associated samples, use terms from the UBERON
          or Plant Ontology to indicate a tissue, organ, or plant structure
    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
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: soil [ENVO:00001998]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - environmental medium
    rank: 8
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000014
    alias: env_medium
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
    any_of:
    - range: EnvMediumSoilEnum
    - range: string
  experimental_factor:
    name: experimental_factor
    annotations:
      expected_value:
        tag: expected_value
        value: text or EFO and/or OBI
    description: Experimental factors are essentially the variable aspects of an experiment
      design which 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). For
      a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;
      for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
    title: experimental factor
    examples:
    - value: time series design [EFO:0001779]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - experimental factor
    rank: 12
    is_a: investigation field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000008
    alias: experimental_factor
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  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: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  extreme_event:
    name: extreme_event
    annotations:
      expected_value:
        tag: expected_value
        value: date, string
    description: Unusual physical events that may have affected microbial populations
    title: history/extreme events
    todos:
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    examples:
    - value: 1980-05-18, volcanic eruption
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/extreme events
    rank: 13
    is_a: core field
    slot_uri: MIXS:0000320
    alias: extreme_event
    owner: SoilInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  fao_class:
    name: fao_class
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil_taxonomic/FAO classification
    rank: 14
    is_a: core field
    slot_uri: MIXS:0001083
    alias: fao_class
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: fao_class_enum
    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: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  fire:
    name: fire
    annotations:
      expected_value:
        tag: expected_value
        value: date string
    description: Historical and/or physical evidence of fire
    title: history/fire
    todos:
    - is "to" acceptable? Is there a better way to request that be written?
    - is "to" acceptable? Is there a better way to request that be written?
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/fire
    rank: 15
    is_a: core field
    slot_uri: MIXS:0001086
    alias: fire
    owner: SoilInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    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:
    name: flooding
    annotations:
      expected_value:
        tag: expected_value
        value: date string
    description: Historical and/or physical evidence of flooding
    title: history/flooding
    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?
    - is "to" acceptable? Is there a better way to request that be written?
    - What about if the "day" isn't known? Is this ok?
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/flooding
    rank: 16
    is_a: core field
    slot_uri: MIXS:0000319
    alias: flooding
    owner: SoilInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  gaseous_environment:
    name: gaseous_environment
    annotations:
      expected_value:
        tag: expected_value
        value: gaseous compound name;gaseous compound amount;treatment interval and
          duration
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: m
    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
    todos:
    - would like to see usage examples for this slot. Requiring micromole/L seems
      too limiting and doesn't match expected_value value
    - did I do this right? keep the example that's provided and add another? so as
      to not override
    - would like to see usage examples for this slot. Requiring micromole/L seems
      too limiting and doesn't match expected_value value
    - did I do this right? keep the example that's provided and add another? so as
      to not override
    examples:
    - value: CO2; 500ppm above ambient; constant
    - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gaseous environment
    rank: 20
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000558
    alias: gaseous_environment
    owner: SoilInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  geo_loc_name:
    name: geo_loc_name
    annotations:
      expected_value:
        tag: expected_value
        value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location
          name'
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name.
    title: geographic location (country and/or sea,region)
    examples:
    - value: 'USA: Maryland, Bethesda'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - geographic location (country and/or sea,region)
    rank: 4
    is_a: environment field
    string_serialization: '{text}: {text}, {text}'
    slot_uri: MIXS:0000010
    alias: geo_loc_name
    owner: SoilInterface
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  growth_facil:
    name: growth_facil
    annotations:
      expected_value:
        tag: expected_value
        value: free text or CO
      occurrence:
        tag: occurrence
        value: '1'
    description: 'Type of facility/location where the sample was harvested; controlled
      vocabulary: growth chamber, open top chamber, glasshouse, experimental garden,
      field.'
    title: growth facility
    notes:
    - 'Removed from description: Alternatively use Crop Ontology (CO) terms'
    examples:
    - value: Growth chamber [CO_715:0000189]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - growth facility
    rank: 1
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001043
    alias: growth_facil
    owner: SoilInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: GrowthFacilEnum
    required: true
    multivalued: false
  heavy_metals:
    name: heavy_metals
    annotations:
      expected_value:
        tag: expected_value
        value: heavy metal name;measurement value unit
      preferred_unit:
        tag: preferred_unit
        value: microgram per gram
      occurrence:
        tag: occurrence
        value: m
    description: Heavy metals present in the sample and their concentrations.
    title: heavy metals/ extreme unusual properties
    todos:
    - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will
      validate?
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
      I would argue this isn't an extreme unusual property. It's just a biogeochemical
      measurement.
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?
    - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
      I would argue this isn't an extreme unusual property. It's just a biogeochemical
      measurement.
    notes:
    - Changed to multi-valued. In MIxS, you add another column to denote multiple
      heavy metals. We don't have that ability in the submission portal.
    comments:
    - For multiple heavy metals and concentrations, separate by ;
    examples:
    - value: mercury 0.09 micrograms per gram
    - value: mercury 0.09 ug/g; chromium 0.03 ug/g
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - extreme_unusual_properties/heavy metals
    rank: 17
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000652
    alias: heavy_metals
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      [^;\t\r\x0A]+)$
  heavy_metals_meth:
    name: heavy_metals_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining heavy metals
    title: heavy metals method/ extreme unusual properties
    todos:
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    comments:
    - Required when heavy metals are provided
    - If different methods are used for multiple metals, indicate the metal and method.
      Separate metals by ;
    examples:
    - value: https://doi.org/10.3390/ijms9040434
    - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - extreme_unusual_properties/heavy metals method
    rank: 18
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000343
    alias: heavy_metals_meth
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  horizon_meth:
    name: horizon_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining the horizon
    title: soil horizon method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil horizon method
    rank: 19
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000321
    alias: horizon_meth
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  humidity_regm:
    name: humidity_regm
    annotations:
      expected_value:
        tag: expected_value
        value: humidity value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram per cubic meter
      occurrence:
        tag: occurrence
        value: m
    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/nmdc/nmdc
    aliases:
    - humidity regimen
    rank: 21
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000568
    alias: humidity_regm
    owner: SoilInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  infiltrations:
    name: infiltrations
    description: The amount of time it takes to complete each infiltration activity
    examples:
    - value: 00:01:32;00:00:53
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1
    aliases:
    - infiltration_1
    - infiltration_2
    rank: 1009
    list_elements_ordered: true
    alias: infiltrations
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^(?:(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9])(?:;(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9])*$
  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: SoilInterface
    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)?)?)?)?$
  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)
    notes:
    - This is currently a required field but it's not clear if this should be required
      for human hosts
    examples:
    - value: 50.586825 6.408977
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - geographic location (latitude and longitude)
    rank: 5
    is_a: environment field
    string_serialization: '{lat lon}'
    slot_uri: MIXS:0000009
    alias: lat_lon
    owner: SoilInterface
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$
  lbc_thirty:
    name: lbc_thirty
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: ppm CaCO3/pH
      occurrence:
        tag: occurrence
        value: '1'
    description: lime buffer capacity, determined after 30 minute incubation
    title: lime buffer capacity (at 30 minutes)
    comments:
    - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by
      one pH unit
    examples:
    - value: 543 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    - https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF
    aliases:
    - lbc_thirty
    - lbc30
    - lime buffer capacity (at 30 minutes)
    rank: 1001
    alias: lbc_thirty
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  lbceq:
    name: lbceq
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: ppm CaCO3/pH
      occurrence:
        tag: occurrence
        value: '1'
    description: lime buffer capacity, determined at equilibrium after 5 day incubation
    title: lime buffer capacity (after 5 day incubation)
    comments:
    - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by
      one pH unit
    examples:
    - value: 1575 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - lbceq
    - lime buffer capacity (at 5-day equilibrium)
    rank: 1002
    alias: lbceq
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about treatment(s) involving exposure to light, including
      both light intensity and quality.
    title: light regimen
    examples:
    - value: incandescant light;10 lux;450 nanometer
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - light regimen
    rank: 24
    is_a: core field
    string_serialization: '{text};{float} {unit};{float} {unit}'
    slot_uri: MIXS:0000569
    alias: light_regm
    owner: SoilInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      \S+$
  link_addit_analys:
    name: link_addit_analys
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Link to additional analysis results performed on the sample
    title: links to additional analysis
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - links to additional analysis
    rank: 56
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000340
    alias: link_addit_analys
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  link_class_info:
    name: link_class_info
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Link to digitized soil maps or other soil classification information
    title: link to classification information
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - link to classification information
    rank: 20
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000329
    alias: link_class_info
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  link_climate_info:
    name: link_climate_info
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Link to climate resource
    title: link to climate information
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - link to climate information
    rank: 21
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000328
    alias: link_climate_info
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  local_class:
    name: local_class
    annotations:
      expected_value:
        tag: expected_value
        value: local classification name
      occurrence:
        tag: occurrence
        value: '1'
    description: Soil classification based on local soil classification system
    title: soil_taxonomic/local classification
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil_taxonomic/local classification
    rank: 22
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000330
    alias: local_class
    owner: SoilInterface
    domain_of:
    - FieldResearchSite
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  local_class_meth:
    name: local_class_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining the local soil classification
    title: soil_taxonomic/local classification method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil_taxonomic/local classification method
    rank: 24
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000331
    alias: local_class_meth
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  manganese:
    name: manganese
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg (ppm)
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of manganese in the sample
    title: manganese
    examples:
    - value: 24.7 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - manganese
    rank: 1003
    alias: manganese
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: SoilInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  micro_biomass_meth:
    name: micro_biomass_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining microbial biomass
    title: microbial biomass method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - microbial biomass method
    rank: 43
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000339
    alias: micro_biomass_meth
    owner: SoilInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    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: SoilInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
  microbial_biomass:
    name: microbial_biomass
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: ton, kilogram, gram per kilogram soil
      occurrence:
        tag: occurrence
        value: '1'
    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
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - microbial biomass
    rank: 42
    is_a: core field
    slot_uri: MIXS:0000650
    alias: microbial_biomass
    owner: SoilInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: SoilInterface
    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: SoilInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
  misc_param:
    name: misc_param
    annotations:
      expected_value:
        tag: expected_value
        value: parameter name;measurement value
      occurrence:
        tag: occurrence
        value: m
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    examples:
    - value: Bicarbonate ion concentration;2075 micromole per kilogram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - miscellaneous parameter
    rank: 23
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    alias: misc_param
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      [^;\t\r\x0A]+)$
  nitrate_nitrogen:
    name: nitrate_nitrogen
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of nitrate nitrogen in the sample
    title: nitrate_nitrogen
    comments:
    - often below some specified limit of detection
    examples:
    - value: 0.29 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - nitrate_nitrogen
    - NO3-N
    rank: 1006
    alias: nitrate_nitrogen
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  nitrite_nitrogen:
    name: nitrite_nitrogen
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of nitrite nitrogen in the sample
    title: nitrite_nitrogen
    examples:
    - value: 1.2 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - nitrite_nitrogen
    - NO2-N
    rank: 1007
    alias: nitrite_nitrogen
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[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: SoilInterface
    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: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
  org_matter:
    name: org_matter
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of organic matter
    title: organic matter
    examples:
    - value: 1.75 milligram per cubic meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organic matter
    rank: 45
    is_a: core field
    slot_uri: MIXS:0000204
    alias: org_matter
    owner: SoilInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  org_nitro:
    name: org_nitro
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of organic nitrogen
    title: organic nitrogen
    examples:
    - value: 4 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organic nitrogen
    rank: 46
    is_a: core field
    slot_uri: MIXS:0000205
    alias: org_nitro
    owner: SoilInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: SoilInterface
    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: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
  oxy_stat_samp:
    name: oxy_stat_samp
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Oxygenation status of sample
    title: oxygenation status of sample
    examples:
    - value: aerobic
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - oxygenation status of sample
    rank: 25
    is_a: core field
    slot_uri: MIXS:0000753
    alias: oxy_stat_samp
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: OxyStatSampEnum
    multivalued: false
  ph:
    name: ph
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    description: pH measurement of the sample, or liquid portion of sample, or aqueous
      phase of the fluid
    title: pH
    notes:
    - Use modified term
    examples:
    - value: '7.2'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pH
    rank: 27
    is_a: core field
    string_serialization: '{float}'
    slot_uri: MIXS:0001001
    alias: ph
    owner: SoilInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: float
    recommended: true
    multivalued: false
    minimum_value: 0
    maximum_value: 14
  ph_meth:
    name: ph_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining ph
    title: pH method
    comments:
    - This can include a link to the instrument used or a citation for the method.
    examples:
    - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB
    - value: https://doi.org/10.2136/sssabookser5.3.c16
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pH method
    rank: 41
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0001106
    alias: ph_meth
    owner: SoilInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  phosphate:
    name: phosphate
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of phosphate
    title: phosphate
    examples:
    - value: 0.7 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - phosphate
    rank: 53
    is_a: core field
    slot_uri: MIXS:0000505
    alias: phosphate
    owner: SoilInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  prev_land_use_meth:
    name: prev_land_use_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining previous land use and dates
    title: history/previous land use method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/previous land use method
    rank: 26
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000316
    alias: prev_land_use_meth
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  previous_land_use:
    name: previous_land_use
    annotations:
      expected_value:
        tag: expected_value
        value: land use name;date
      occurrence:
        tag: occurrence
        value: '1'
    description: Previous land use and dates
    title: history/previous land use
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/previous land use
    rank: 27
    is_a: core field
    string_serialization: '{text};{timestamp}'
    slot_uri: MIXS:0000315
    alias: previous_land_use
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^\S+.*\S+;([\+-]?\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)?)?)?)?$
  profile_position:
    name: profile_position
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - profile position
    rank: 28
    is_a: core field
    slot_uri: MIXS:0001084
    alias: profile_position
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: profile_position_enum
    multivalued: false
  salinity:
    name: salinity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: practical salinity unit, percentage
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - salinity
    rank: 54
    is_a: core field
    slot_uri: MIXS:0000183
    alias: salinity
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  salinity_meth:
    name: salinity_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining salinity
    title: salinity method
    examples:
    - value: https://doi.org/10.1007/978-1-61779-986-0_28
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - salinity method
    rank: 55
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000341
    alias: salinity_meth
    owner: SoilInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  samp_collec_device:
    name: samp_collec_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
    comments:
    - Report dimensions and details when applicable
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample collection device
    rank: 14
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000002
    alias: samp_collec_device
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  samp_collec_method:
    name: samp_collec_method
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url , or text
    description: The method employed for collecting the sample.
    title: sample collection method
    comments:
    - This can be a citation or description
    examples:
    - value: swabbing
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample collection method
    rank: 15
    is_a: nucleic acid sequence source field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001225
    alias: samp_collec_method
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
  samp_mat_process:
    name: samp_mat_process
    annotations:
      expected_value:
        tag: expected_value
        value: text
    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
    - value: storing samples in ethanol
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample material processing
    rank: 12
    is_a: nucleic acid sequence source field
    string_serialization: '{text}'
    slot_uri: MIXS:0000016
    alias: samp_mat_process
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
  samp_size:
    name: samp_size
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millliter, gram, milligram, liter
    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
      sample collected.
    title: amount or size of sample collected
    comments:
    - This refers to the TOTAL amount of sample collected from the experiment. NOT
      the amount sent to each institution or collected for a specific analysis.
    examples:
    - value: 5 grams
    - value: 10 mL
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - amount or size of sample collected
    rank: 18
    is_a: nucleic acid sequence source field
    string_serialization: '{float} {unit}'
    slot_uri: MIXS:0000001
    alias: samp_size
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
  samp_store_temp:
    name: samp_store_temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: '1'
    description: Temperature at which the sample was stored (degrees are assumed)
    title: sample storage temperature
    examples:
    - value: -80 Celsius
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample storage temperature
    rank: 7
    is_a: core field
    slot_uri: MIXS:0000110
    alias: samp_store_temp
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  sample_link:
    name: sample_link
    description: A unique identifier to assign parent-child, subsample, or sibling
      samples. This is relevant when a sample or other material was used to generate
      the new sample.
    title: sample linkage
    notes:
    - 'also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) >
      1 and "placeholder" in slot_usage.keys():AttributeError: ''list'' object has
      no attribute ''keys'''
    comments:
    - 'This field allows multiple entries separated by ; (Examples: Soil collected
      from the field will link with the soil used in an incubation. The soil a plant
      was grown in links to the plant sample. An original culture sample was transferred
      to a new vial and generated a new sample)'
    examples:
    - value: IGSN:DSJ0284
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 5
    string_serialization: '{text}:{text}'
    alias: sample_link
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    - SampIdNewTermsMixin
    slot_group: sample_id_section
    range: string
    recommended: true
    multivalued: false
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'
  season_precpt:
    name: season_precpt
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millimeter
      occurrence:
        tag: occurrence
        value: '1'
    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: average seasonal precipitation
    todos:
    - check validation & examples. always mm? so value only? Or value + unit
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    - check validation & examples. always mm? so value only? Or value + unit
    notes:
    - mean and average are the same thing, but it seems like bad practice to not be
      consistent. Changed mean to average
    - mean and average are the same thing, but it seems like bad practice to not be
      consistent. Changed mean to average
    comments:
    - Seasons are defined as spring (March, April, May), summer (June, July, August),
      autumn (September, October, November) and winter (December, January, February).
    examples:
    - value: 0.4 inch
    - value: 10.16 mm
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean seasonal precipitation
    rank: 29
    is_a: core field
    slot_uri: MIXS:0000645
    alias: season_precpt
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  season_temp:
    name: season_temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: '1'
    description: Mean seasonal temperature
    title: mean seasonal temperature
    examples:
    - value: 18 degree Celsius
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean seasonal temperature
    rank: 30
    is_a: core field
    slot_uri: MIXS:0000643
    alias: season_temp
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  sieving:
    name: sieving
    annotations:
      expected_value:
        tag: expected_value
        value: design name and/or size;amount
      occurrence:
        tag: occurrence
        value: '1'
    description: Collection design of pooled samples and/or sieve size and amount
      of sample sieved
    title: composite design/sieving
    todos:
    - check validation and examples
    - check validation and examples
    comments:
    - Describe how samples were composited or sieved.
    - Use 'sample link' to indicate which samples were combined.
    examples:
    - value: combined 2 cores
    - value: 4mm sieved
    - value: 4 mm sieved and homogenized
    - value: 50 g
    - value: 5 cores
    - value: 2 mm sieved
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - composite design/sieving
    rank: 8
    is_a: core field
    string_serialization: '{{text}|{float} {unit}};{float} {unit}'
    slot_uri: MIXS:0000322
    alias: sieving
    owner: SoilInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  size_frac_low:
    name: size_frac_low
    annotations:
      expected_value:
        tag: expected_value
        value: value
      preferred_unit:
        tag: preferred_unit
        value: micrometer
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - size-fraction lower threshold
    rank: 10
    is_a: core field
    slot_uri: MIXS:0000735
    alias: size_frac_low
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: false
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  size_frac_up:
    name: size_frac_up
    annotations:
      expected_value:
        tag: expected_value
        value: value
      preferred_unit:
        tag: preferred_unit
        value: micrometer
      occurrence:
        tag: occurrence
        value: '1'
    description: Refers to the mesh/pore size 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/nmdc/nmdc
    aliases:
    - size-fraction upper threshold
    rank: 11
    is_a: core field
    slot_uri: MIXS:0000736
    alias: size_frac_up
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: false
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  slope_aspect:
    name: slope_aspect
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree
      occurrence:
        tag: occurrence
        value: '1'
    description: The direction a slope faces. While looking down a slope use a compass
      to record the direction you are facing (direction or degrees). - This measure
      provides an indication of sun and wind exposure that will influence soil temperature
      and evapotranspiration.
    title: slope aspect
    todos:
    - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,
      map this to the MIxS slot
    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.
    examples:
    - value: '35'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - slope aspect
    rank: 1
    is_a: core field
    slot_uri: MIXS:0000647
    alias: slope_aspect
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  slope_gradient:
    name: slope_gradient
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: percentage
      occurrence:
        tag: occurrence
        value: '1'
    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
    todos:
    - Slope is a percent. How does the validation work? Check to correct examples
    - Slope is a percent. How does the validation work? Check to correct examples
    examples:
    - value: 10%
    - value: 10 %
    - value: '0.1'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - slope gradient
    rank: 31
    is_a: core field
    slot_uri: MIXS:0000646
    alias: slope_gradient
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  soil_horizon:
    name: soil_horizon
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - soil horizon
    rank: 32
    is_a: core field
    slot_uri: MIXS:0001082
    alias: soil_horizon
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: soil_horizon_enum
    multivalued: false
  soil_text_measure:
    name: soil_text_measure
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    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 measurement
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil texture measurement
    rank: 33
    is_a: core field
    slot_uri: MIXS:0000335
    alias: soil_text_measure
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  soil_texture_meth:
    name: soil_texture_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining soil texture
    title: soil texture method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil texture method
    rank: 34
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000336
    alias: soil_texture_meth
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  soil_type:
    name: soil_type
    annotations:
      expected_value:
        tag: expected_value
        value: ENVO_00001998
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - soil type
    rank: 35
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000332
    alias: soil_type
    owner: SoilInterface
    domain_of:
    - FieldResearchSite
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  soil_type_meth:
    name: soil_type_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining soil series name or other
      lower-level classification
    title: soil type method
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soil type method
    rank: 36
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000334
    alias: soil_type_meth
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  specific_ecosystem:
    name: specific_ecosystem
    description: Specific ecosystems represent specific features of the environment
      like aphotic zone in an ocean or gastric mucosa within a host digestive system.
      Specific ecosystem is in position 5/5 in a GOLD path.
    comments:
    - Specific ecosystems help to define samples based on very specific characteristics
      of an environment under the five-level classification system.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 13
    is_a: gold_path_field
    alias: specific_ecosystem
    owner: SoilInterface
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: SpecificEcosystemForSoilEnum
    recommended: true
  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: SoilInterface
    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: SoilInterface
    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?$)):([0-5]\d)(:([0-5]\d))?$
  store_cond:
    name: store_cond
    annotations:
      expected_value:
        tag: expected_value
        value: storage condition type;duration
      occurrence:
        tag: occurrence
        value: '1'
    description: Explain how the soil sample is stored (fresh/frozen/other).
    title: storage conditions
    examples:
    - value: -20 degree Celsius freezer;P2Y10D
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - storage conditions
    rank: 2
    is_a: core field
    string_serialization: '{text};{duration}'
    slot_uri: MIXS:0000327
    alias: store_cond
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_modified_section
    range: StoreCondEnum
    required: true
    multivalued: false
  temp:
    name: temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      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
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - temperature
    rank: 37
    is_a: environment field
    slot_uri: MIXS:0000113
    alias: temp
    owner: SoilInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tillage:
    name: tillage
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: m
    description: Note method(s) used for tilling
    title: history/tillage
    examples:
    - value: chisel
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - history/tillage
    rank: 38
    is_a: core field
    slot_uri: MIXS:0001081
    alias: tillage
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_section
    range: tillage_enum
    multivalued: true
  tot_carb:
    name: tot_carb
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Total carbon content
    title: total carbon
    todos:
    - is this inorganic and organic? both? could use some clarification.
    - ug/L doesn't seem like the right units. Should check this slots usage in databases
      and re-evaluate. I couldn't find any references that provided this data in this
      format
    - is this inorganic and organic? both? could use some clarification.
    - ug/L doesn't seem like the right units. Should check this slots usage in databases
      and re-evaluate. I couldn't find any references that provided this data in this
      format
    examples:
    - value: 1 ug/L
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total carbon
    rank: 47
    is_a: core field
    slot_uri: MIXS:0000525
    alias: tot_carb
    owner: SoilInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tot_nitro_cont_meth:
    name: tot_nitro_cont_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining the total nitrogen
    title: total nitrogen content method
    examples:
    - value: https://doi.org/10.2134/agronmonogr9.2.c32
    - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total nitrogen content method
    rank: 49
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000338
    alias: tot_nitro_cont_meth
    owner: SoilInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  tot_nitro_content:
    name: tot_nitro_content
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, micromole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Total nitrogen content of the sample
    title: total nitrogen content
    examples:
    - value: 5 mg N/ L
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total nitrogen content
    rank: 48
    is_a: core field
    slot_uri: MIXS:0000530
    alias: tot_nitro_content
    owner: SoilInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tot_org_c_meth:
    name: tot_org_c_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining total organic carbon
    title: total organic carbon method
    examples:
    - value: https://doi.org/10.1080/07352680902776556
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total organic carbon method
    rank: 51
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000337
    alias: tot_org_c_meth
    owner: SoilInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  tot_org_carb:
    name: tot_org_carb
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram Carbon per kilogram sample material
      occurrence:
        tag: occurrence
        value: '1'
    description: 'Definition for soil: total organic carbon content of the soil, definition
      otherwise: total organic carbon content'
    title: total organic carbon
    todos:
    - check description. How are they different?
    - check description. How are they different?
    examples:
    - value: 5 mg N/ L
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total organic carbon
    rank: 50
    is_a: core field
    slot_uri: MIXS:0000533
    alias: tot_org_carb
    owner: SoilInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tot_phosp:
    name: tot_phosp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter, milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    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/nmdc/nmdc
    aliases:
    - total phosphorus
    rank: 52
    is_a: core field
    slot_uri: MIXS:0000117
    alias: tot_phosp
    owner: SoilInterface
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  water_cont_soil_meth:
    name: water_cont_soil_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining the water content of soil
    title: water content method
    todos:
    - Why is it soil water content method in the name but not the title? Is this slot
      used in other samples?
    - Soil water content can be measure MANY ways and often, multiple ways are used
      in one experiment (gravimetric water content and water holding capacity and
      water filled pore space, to name a few).
    - Should this be multi valued? How to we manage and validate this?
    - Why is it soil water content method in the name but not the title? Is this slot
      used in other samples?
    - Soil water content can be measure MANY ways and often, multiple ways are used
      in one experiment (gravimetric water content and water holding capacity and
      water filled pore space, to name a few).
    - Should this be multi valued? How to we manage and validate this?
    comments:
    - Required if providing water content
    examples:
    - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503
    - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - water content method
    rank: 40
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000323
    alias: water_cont_soil_meth
    owner: SoilInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  water_content:
    name: water_content
    annotations:
      expected_value:
        tag: expected_value
        value: string
      preferred_unit:
        tag: preferred_unit
        value: gram per gram or cubic centimeter per cubic centimeter
    description: Water content measurement
    title: water content
    todos:
    - value in preferred unit is too limiting. need to change this
    - check and correct validation so examples are accepted
    - how to manage multiple water content methods?
    examples:
    - value: 0.75 g water/g dry soil
    - value: 75% water holding capacity
    - value: 1.1 g fresh weight/ dry weight
    - value: 10% water filled pore space
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - water content
    rank: 39
    is_a: core field
    string_serialization: '{float or pct} {unit}'
    slot_uri: MIXS:0000185
    alias: water_content
    owner: SoilInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?%? \S.+$
  watering_regm:
    name: watering_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: milliliter, liter
      occurrence:
        tag: occurrence
        value: m
    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
    - value: 75% water holding capacity; constant
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - watering regimen
    rank: 25
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000591
    alias: watering_regm
    owner: SoilInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  zinc:
    name: zinc
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mg/kg (ppm)
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of zinc in the sample
    title: zinc
    examples:
    - value: 2.5 mg/kg
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://www.ornl.gov/content/bio-scales-0
    aliases:
    - zinc
    rank: 1004
    alias: zinc
    owner: SoilInterface
    domain_of:
    - Biosample
    - SoilInterface
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  analysis_type:
    name: analysis_type
    description: Select all the data types associated or available for this biosample
    title: analysis/data type
    examples:
    - value: metagenomics; metabolomics; proteomics
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIxS:investigation_type
    rank: 3
    alias: analysis_type
    owner: SoilInterface
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: AnalysisTypeEnum
    required: true
    recommended: false
    multivalued: true
  samp_name:
    name: samp_name
    annotations:
      expected_value:
        tag: expected_value
        value: text
    description: A local identifier or name that for the material sample collected.
      Refers to the original material collected or to any derived sub-samples.
    title: sample name
    comments:
    - It can have any format, but we suggest that you make it concise, unique and
      consistent within your lab, and as informative as possible.
    examples:
    - value: Rock core CB1178(5-6) from NSW
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample name
    rank: 1
    is_a: investigation field
    string_serialization: '{text}'
    slot_uri: MIXS:0001107
    identifier: true
    alias: samp_name
    owner: SoilInterface
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    required: true
    multivalued: false
  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 globally unique identifier assigned to the biological sample.
    title: source material identifier
    todos:
    - Currently, the comments say to use UUIDs. However, if we implement assigning
      NMDC identifiers with the minter we dont need to require a GUID. It can be an
      optional field to fill out only if they already have a resolvable ID.
    - Currently, the comments say to use UUIDs. However, if we implement assigning
      NMDC identifiers with the minter we dont need to require a GUID. It can be an
      optional field to fill out only if they already have a resolvable ID.
    notes:
    - The source material IS the Globally Unique ID
    comments:
    - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),
      NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These
      IDs enable linking to derived analytes and subsamples. If you have not assigned
      FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).
    - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),
      NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These
      IDs enable linking to derived analytes and subsamples. If you have not assigned
      FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).
    examples:
    - value: IGSN:AU1243
    - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - source material identifiers
    rank: 2
    is_a: nucleic acid sequence source field
    string_serialization: '{text}:{text}'
    slot_uri: MIXS:0000026
    alias: source_mat_id
    owner: SoilInterface
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    multivalued: false
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'