Class: Sediment (SedimentInterface)

name: SedimentInterface
annotations:
  excel_worksheet_name:
    tag: excel_worksheet_name
    value: sediment
description: sediment dh_interface
title: Sediment
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
- SampIdNewTermsMixin
slots:
- air_temp_regm
- alkalinity
- alkalinity_method
- alkyl_diethers
- aminopept_act
- ammonium
- bacteria_carb_prod
- biomass
- biotic_regm
- biotic_relationship
- bishomohopanol
- bromide
- calcium
- carb_nitro_ratio
- chem_administration
- chloride
- chlorophyll
- climate_environment
- collection_date
- collection_date_inc
- collection_time
- density
- depth
- diether_lipids
- diss_carb_dioxide
- diss_hydrogen
- diss_inorg_carb
- diss_org_carb
- diss_org_nitro
- diss_oxygen
- ecosystem
- ecosystem_category
- ecosystem_subtype
- ecosystem_type
- elev
- env_broad_scale
- env_local_scale
- env_medium
- experimental_factor
- extreme_event
- fire
- flooding
- gaseous_environment
- geo_loc_name
- glucosidase_act
- humidity_regm
- isotope_exposure
- lat_lon
- light_regm
- magnesium
- mean_frict_vel
- mean_peak_frict_vel
- methane
- micro_biomass_c_meth
- micro_biomass_meth
- micro_biomass_n_meth
- microbial_biomass
- microbial_biomass_c
- microbial_biomass_n
- misc_param
- n_alkanes
- nitrate
- nitrite
- nitro
- org_carb
- org_matter
- org_nitro
- org_nitro_method
- organism_count
- oxy_stat_samp
- part_org_carb
- particle_class
- perturbation
- petroleum_hydrocarb
- ph
- ph_meth
- phaeopigments
- phosphate
- phosplipid_fatt_acid
- porosity
- potassium
- pressure
- redox_potential
- salinity
- salinity_meth
- samp_collec_device
- samp_collec_method
- samp_mat_process
- samp_size
- samp_store_dur
- samp_store_loc
- samp_store_temp
- sample_link
- sediment_type
- sieving
- silicate
- size_frac
- sodium
- specific_ecosystem
- start_date_inc
- sulfate
- sulfide
- temp
- tidal_stage
- tot_carb
- tot_depth_water_col
- tot_nitro_cont_meth
- tot_nitro_content
- tot_org_c_meth
- tot_org_carb
- turbidity
- water_cont_soil_meth
- water_content
- watering_regm
slot_usage:
  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
    multivalued: false
  alkalinity:
    name: alkalinity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milliequivalent per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Alkalinity, the ability of a solution to neutralize acids to the
      equivalence point of carbonate or bicarbonate
    title: alkalinity
    examples:
    - value: 50 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - alkalinity
    rank: 1
    is_a: core field
    slot_uri: MIXS:0000421
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  alkalinity_method:
    name: alkalinity_method
    annotations:
      expected_value:
        tag: expected_value
        value: description of method
      occurrence:
        tag: occurrence
        value: '1'
    description: Method used for alkalinity measurement
    title: alkalinity method
    examples:
    - value: titration
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - alkalinity method
    rank: 218
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000298
    owner: Biosample
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  alkyl_diethers:
    name: alkyl_diethers
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of alkyl diethers
    title: alkyl diethers
    examples:
    - value: 0.005 mole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - alkyl diethers
    rank: 2
    is_a: core field
    slot_uri: MIXS:0000490
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  aminopept_act:
    name: aminopept_act
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per liter per hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of aminopeptidase activity
    title: aminopeptidase activity
    examples:
    - value: 0.269 mole per liter per hour
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - aminopeptidase activity
    rank: 3
    is_a: core field
    slot_uri: MIXS:0000172
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  ammonium:
    name: ammonium
    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: Concentration of ammonium in the sample
    title: ammonium
    examples:
    - value: 1.5 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - ammonium
    rank: 4
    is_a: core field
    slot_uri: MIXS:0000427
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  bacteria_carb_prod:
    name: bacteria_carb_prod
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: nanogram per hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of bacterial carbon production
    title: bacterial carbon production
    examples:
    - value: 2.53 microgram per liter per hour
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - bacterial carbon production
    rank: 5
    is_a: core field
    slot_uri: MIXS:0000173
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  biomass:
    name: biomass
    annotations:
      expected_value:
        tag: expected_value
        value: biomass type;measurement value
      preferred_unit:
        tag: preferred_unit
        value: ton, kilogram, gram
      occurrence:
        tag: occurrence
        value: m
    description: Amount of biomass; should include the name for the part of biomass
      measured, e.g. Microbial, total. Can include multiple measurements
    title: biomass
    examples:
    - value: total;20 gram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - biomass
    rank: 6
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000174
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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]+)$
  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
    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
  bishomohopanol:
    name: bishomohopanol
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, microgram per gram
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of bishomohopanol
    title: bishomohopanol
    examples:
    - value: 14 microgram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - bishomohopanol
    rank: 7
    is_a: core field
    slot_uri: MIXS:0000175
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  bromide:
    name: bromide
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of bromide
    title: bromide
    examples:
    - value: 0.05 parts per million
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - bromide
    rank: 8
    is_a: core field
    slot_uri: MIXS:0000176
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  calcium:
    name: calcium
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter, micromole per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of calcium in the sample
    title: calcium
    examples:
    - value: 0.2 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - calcium
    rank: 9
    is_a: core field
    slot_uri: MIXS:0000432
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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)?)?)?)?$
  chloride:
    name: chloride
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of chloride in the sample
    title: chloride
    examples:
    - value: 5000 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chloride
    rank: 10
    is_a: core field
    slot_uri: MIXS:0000429
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  chlorophyll:
    name: chlorophyll
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per cubic meter, microgram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of chlorophyll
    title: chlorophyll
    examples:
    - value: 5 milligram per cubic meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chlorophyll
    rank: 11
    is_a: core field
    slot_uri: MIXS:0000177
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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.
    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
    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?$)):([0-5]\d)(:([0-5]\d))?$
  density:
    name: density
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram per cubic meter, gram per cubic centimeter
      occurrence:
        tag: occurrence
        value: '1'
    description: Density of the sample, which is its mass per unit volume (aka volumetric
      mass density)
    title: density
    examples:
    - value: 1000 kilogram per cubic meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - density
    rank: 12
    is_a: core field
    slot_uri: MIXS:0000435
    owner: Biosample
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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]+)?$
  diether_lipids:
    name: diether_lipids
    annotations:
      expected_value:
        tag: expected_value
        value: diether lipid name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: nanogram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of diether lipids; can include multiple types of diether
      lipids
    title: diether lipids
    examples:
    - value: 0.2 nanogram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - diether lipids
    rank: 13
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000178
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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]+)$
  diss_carb_dioxide:
    name: diss_carb_dioxide
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of dissolved carbon dioxide in the sample or liquid
      portion of the sample
    title: dissolved carbon dioxide
    examples:
    - value: 5 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved carbon dioxide
    rank: 14
    is_a: core field
    slot_uri: MIXS:0000436
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_hydrogen:
    name: diss_hydrogen
    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 dissolved hydrogen
    title: dissolved hydrogen
    examples:
    - value: 0.3 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved hydrogen
    rank: 15
    is_a: core field
    slot_uri: MIXS:0000179
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_inorg_carb:
    name: diss_inorg_carb
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Dissolved inorganic carbon concentration in the sample, typically
      measured after filtering the sample using a 0.45 micrometer filter
    title: dissolved inorganic carbon
    examples:
    - value: 2059 micromole per kilogram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved inorganic carbon
    rank: 16
    is_a: core field
    slot_uri: MIXS:0000434
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_org_carb:
    name: diss_org_carb
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of dissolved organic carbon in the sample, liquid portion
      of the sample, or aqueous phase of the fluid
    title: dissolved organic carbon
    examples:
    - value: 197 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved organic carbon
    rank: 17
    is_a: core field
    slot_uri: MIXS:0000433
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_org_nitro:
    name: diss_org_nitro
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Dissolved organic nitrogen concentration measured as; total dissolved
      nitrogen - NH4 - NO3 - NO2
    title: dissolved organic nitrogen
    examples:
    - value: 0.05 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved organic nitrogen
    rank: 18
    is_a: core field
    slot_uri: MIXS:0000162
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_oxygen:
    name: diss_oxygen
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per kilogram, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of dissolved oxygen
    title: dissolved oxygen
    examples:
    - value: 175 micromole per kilogram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved oxygen
    rank: 19
    is_a: core field
    slot_uri: MIXS:0000119
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: EcosystemEnum
    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: EcosystemCategoryEnum
    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: EcosystemSubtypeEnum
    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: EcosystemTypeEnum
    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
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  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
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  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
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  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: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
  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
    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
  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?
    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?
    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
    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
    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: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  glucosidase_act:
    name: glucosidase_act
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mol per liter per hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of glucosidase activity
    title: glucosidase activity
    examples:
    - value: 5 mol per liter per hour
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - glucosidase activity
    rank: 20
    is_a: core field
    slot_uri: MIXS:0000137
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
    multivalued: false
  isotope_exposure:
    name: isotope_exposure
    description: List isotope exposure or addition applied to your sample.
    title: isotope exposure/addition
    todos:
    - Can we make the H218O correctly super and subscripted?
    comments:
    - This is required when your experimental design includes the use of isotopically
      labeled compounds
    examples:
    - value: 13C glucose
    - value: H218O
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000751
    rank: 16
    string_serialization: '{termLabel} {[termID]}; {timestamp}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
  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})?)$
  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
    multivalued: false
    pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      \S+$
  magnesium:
    name: magnesium
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per liter, milligram per liter, parts per million, micromole per
          kilogram
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of magnesium in the sample
    title: magnesium
    examples:
    - value: 52.8 micromole per kilogram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - magnesium
    rank: 21
    is_a: core field
    slot_uri: MIXS:0000431
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  mean_frict_vel:
    name: mean_frict_vel
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: meter per second
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of mean friction velocity
    title: mean friction velocity
    examples:
    - value: 0.5 meter per second
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean friction velocity
    rank: 22
    is_a: core field
    slot_uri: MIXS:0000498
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  mean_peak_frict_vel:
    name: mean_peak_frict_vel
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: meter per second
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of mean peak friction velocity
    title: mean peak friction velocity
    examples:
    - value: 1 meter per second
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean peak friction velocity
    rank: 23
    is_a: core field
    slot_uri: MIXS:0000502
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  methane:
    name: methane
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter, parts per billion, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Methane (gas) amount or concentration at the time of sampling
    title: methane
    examples:
    - value: 1800 parts per billion
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - methane
    rank: 24
    is_a: core field
    slot_uri: MIXS:0000101
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - SedimentInterface
    slot_group: mixs_core_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]+)$
  n_alkanes:
    name: n_alkanes
    annotations:
      expected_value:
        tag: expected_value
        value: n-alkane name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of n-alkanes; can include multiple n-alkanes
    title: n-alkanes
    examples:
    - value: n-hexadecane;100 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - n-alkanes
    rank: 25
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000503
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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:
    name: nitrate
    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: Concentration of nitrate in the sample
    title: nitrate
    examples:
    - value: 65 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - nitrate
    rank: 26
    is_a: core field
    slot_uri: MIXS:0000425
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  nitrite:
    name: nitrite
    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: Concentration of nitrite in the sample
    title: nitrite
    examples:
    - value: 0.5 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - nitrite
    rank: 27
    is_a: core field
    slot_uri: MIXS:0000426
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  nitro:
    name: nitro
    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 nitrogen (total)
    title: nitrogen
    examples:
    - value: 4.2 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - nitrogen
    rank: 28
    is_a: core field
    slot_uri: MIXS:0000504
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  org_carb:
    name: org_carb
    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 organic carbon
    title: organic carbon
    examples:
    - value: 1.5 microgram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organic carbon
    rank: 29
    is_a: core field
    slot_uri: MIXS:0000508
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
  organism_count:
    name: organism_count
    annotations:
      expected_value:
        tag: expected_value
        value: organism name;measurement value;enumeration
      preferred_unit:
        tag: preferred_unit
        value: number of cells per cubic meter, number of cells per milliliter, number
          of cells per cubic centimeter
      occurrence:
        tag: occurrence
        value: m
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organism count
    rank: 30
    is_a: core field
    slot_uri: MIXS:0000103
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$
  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
  part_org_carb:
    name: part_org_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: Concentration of particulate organic carbon
    title: particulate organic carbon
    examples:
    - value: 1.92 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - particulate organic carbon
    rank: 31
    is_a: core field
    slot_uri: MIXS:0000515
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  particle_class:
    name: particle_class
    annotations:
      expected_value:
        tag: expected_value
        value: particle name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: micrometer
      occurrence:
        tag: occurrence
        value: m
    description: Particles are classified, based on their size, into six general categories:clay,
      silt, sand, gravel, cobbles, and boulders; should include amount of particle
      preceded by the name of the particle type; can include multiple values
    title: particle classification
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - particle classification
    rank: 32
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000206
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    slot_group: mixs_core_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]+)$
  perturbation:
    name: perturbation
    annotations:
      expected_value:
        tag: expected_value
        value: perturbation type name;perturbation interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Type of perturbation, e.g. chemical administration, physical disturbance,
      etc., coupled with perturbation regimen including how many times the perturbation
      was repeated, how long each perturbation lasted, and the start and end time
      of the entire perturbation period; can include multiple perturbation types
    title: perturbation
    examples:
    - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - perturbation
    rank: 33
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000754
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  petroleum_hydrocarb:
    name: petroleum_hydrocarb
    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 petroleum hydrocarbon
    title: petroleum hydrocarbon
    examples:
    - value: 0.05 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - petroleum hydrocarbon
    rank: 34
    is_a: core field
    slot_uri: MIXS:0000516
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
  phaeopigments:
    name: phaeopigments
    annotations:
      expected_value:
        tag: expected_value
        value: phaeopigment name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per cubic meter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of phaeopigments; can include multiple phaeopigments
    title: phaeopigments
    examples:
    - value: 2.5 milligram per cubic meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - phaeopigments
    rank: 35
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000180
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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]+)$
  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.*$
  phosplipid_fatt_acid:
    name: phosplipid_fatt_acid
    annotations:
      expected_value:
        tag: expected_value
        value: phospholipid fatty acid name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per gram, mole per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of phospholipid fatty acids; can include multiple values
    title: phospholipid fatty acid
    examples:
    - value: 2.98 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - phospholipid fatty acid
    rank: 36
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000181
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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]+)$
  porosity:
    name: porosity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value or range
      preferred_unit:
        tag: preferred_unit
        value: percentage
      occurrence:
        tag: occurrence
        value: '1'
    description: Porosity of deposited sediment is volume of voids divided by the
      total volume of sample
    title: porosity
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - porosity
    rank: 37
    is_a: core field
    string_serialization: '{float} - {float} {unit}'
    slot_uri: MIXS:0000211
    owner: Biosample
    domain_of:
    - Biosample
    - HcrCoresInterface
    - SedimentInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  potassium:
    name: potassium
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of potassium in the sample
    title: potassium
    examples:
    - value: 463 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - potassium
    rank: 38
    is_a: core field
    slot_uri: MIXS:0000430
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  pressure:
    name: pressure
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: atmosphere
      occurrence:
        tag: occurrence
        value: '1'
    description: Pressure to which the sample is subject to, in atmospheres
    title: pressure
    examples:
    - value: 50 atmosphere
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pressure
    rank: 39
    is_a: core field
    slot_uri: MIXS:0000412
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  redox_potential:
    name: redox_potential
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millivolt
      occurrence:
        tag: occurrence
        value: '1'
    description: Redox potential, measured relative to a hydrogen cell, indicating
      oxidation or reduction potential
    title: redox potential
    examples:
    - value: 300 millivolt
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - redox potential
    rank: 40
    is_a: core field
    slot_uri: MIXS:0000182
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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_dur:
    name: samp_store_dur
    annotations:
      expected_value:
        tag: expected_value
        value: duration
      occurrence:
        tag: occurrence
        value: '1'
    description: Duration for which the sample was stored
    title: sample storage duration
    examples:
    - value: P1Y6M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample storage duration
    rank: 353
    is_a: core field
    string_serialization: '{duration}'
    slot_uri: MIXS:0000116
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  samp_store_loc:
    name: samp_store_loc
    annotations:
      expected_value:
        tag: expected_value
        value: location name
      occurrence:
        tag: occurrence
        value: '1'
    description: Location at which sample was stored, usually name of a specific freezer/room
    title: sample storage location
    examples:
    - value: Freezer no:5
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample storage location
    rank: 41
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000755
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  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]+'
  sediment_type:
    name: sediment_type
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about the sediment type based on major constituents
    title: sediment type
    examples:
    - value: biogenous
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sediment type
    rank: 42
    is_a: core field
    slot_uri: MIXS:0001078
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    slot_group: mixs_core_section
    range: sediment_type_enum
    multivalued: false
  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
    comments:
    - Describe how samples were composited or sieved.
    - Use 'sample link' to indicate which samples were combined.
    examples:
    - value: combined 2 cores | 4mm sieved
    - value: 4 mm sieved and homogenized
    - value: 50 g | 5 cores | 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
    multivalued: false
  silicate:
    name: silicate
    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 silicate
    title: silicate
    examples:
    - value: 0.05 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - silicate
    rank: 43
    is_a: core field
    slot_uri: MIXS:0000184
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  size_frac:
    name: size_frac
    annotations:
      expected_value:
        tag: expected_value
        value: filter size value range
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    examples:
    - value: 0-0.22 micrometer
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - size fraction selected
    rank: 285
    is_a: nucleic acid sequence source field
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  sodium:
    name: sodium
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Sodium concentration in the sample
    title: sodium
    examples:
    - value: 10.5 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sodium
    rank: 363
    is_a: core field
    slot_uri: MIXS:0000428
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: SpecificEcosystemEnum
    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]))?)?$
  sulfate:
    name: sulfate
    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: Concentration of sulfate in the sample
    title: sulfate
    examples:
    - value: 5 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sulfate
    rank: 44
    is_a: core field
    slot_uri: MIXS:0000423
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  sulfide:
    name: sulfide
    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: Concentration of sulfide in the sample
    title: sulfide
    examples:
    - value: 2 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sulfide
    rank: 371
    is_a: core field
    slot_uri: MIXS:0000424
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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.*$
  tidal_stage:
    name: tidal_stage
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Stage of tide
    title: tidal stage
    examples:
    - value: high tide
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - tidal stage
    rank: 45
    is_a: core field
    slot_uri: MIXS:0000750
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: tidal_stage_enum
    multivalued: false
  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_depth_water_col:
    name: tot_depth_water_col
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: meter
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of total depth of water column
    title: total depth of water column
    examples:
    - value: 500 meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total depth of water column
    rank: 46
    is_a: core field
    slot_uri: MIXS:0000634
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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.*$
  turbidity:
    name: turbidity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: formazin turbidity unit, formazin nephelometric units
      occurrence:
        tag: occurrence
        value: '1'
    description: Measure of the amount of cloudiness or haziness in water caused by
      individual particles
    title: turbidity
    examples:
    - value: 0.3 nephelometric turbidity units
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - turbidity
    rank: 47
    is_a: core field
    slot_uri: MIXS:0000191
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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?
    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
    multivalued: false
  horizon_meth:
    name: horizon_meth
    title: horizon method

name: SedimentInterface
annotations:
  excel_worksheet_name:
    tag: excel_worksheet_name
    value: sediment
description: sediment dh_interface
title: Sediment
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
- SampIdNewTermsMixin
slot_usage:
  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
    multivalued: false
  alkalinity:
    name: alkalinity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milliequivalent per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Alkalinity, the ability of a solution to neutralize acids to the
      equivalence point of carbonate or bicarbonate
    title: alkalinity
    examples:
    - value: 50 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - alkalinity
    rank: 1
    is_a: core field
    slot_uri: MIXS:0000421
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  alkalinity_method:
    name: alkalinity_method
    annotations:
      expected_value:
        tag: expected_value
        value: description of method
      occurrence:
        tag: occurrence
        value: '1'
    description: Method used for alkalinity measurement
    title: alkalinity method
    examples:
    - value: titration
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - alkalinity method
    rank: 218
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000298
    owner: Biosample
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  alkyl_diethers:
    name: alkyl_diethers
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of alkyl diethers
    title: alkyl diethers
    examples:
    - value: 0.005 mole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - alkyl diethers
    rank: 2
    is_a: core field
    slot_uri: MIXS:0000490
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  aminopept_act:
    name: aminopept_act
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per liter per hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of aminopeptidase activity
    title: aminopeptidase activity
    examples:
    - value: 0.269 mole per liter per hour
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - aminopeptidase activity
    rank: 3
    is_a: core field
    slot_uri: MIXS:0000172
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  ammonium:
    name: ammonium
    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: Concentration of ammonium in the sample
    title: ammonium
    examples:
    - value: 1.5 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - ammonium
    rank: 4
    is_a: core field
    slot_uri: MIXS:0000427
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  bacteria_carb_prod:
    name: bacteria_carb_prod
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: nanogram per hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of bacterial carbon production
    title: bacterial carbon production
    examples:
    - value: 2.53 microgram per liter per hour
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - bacterial carbon production
    rank: 5
    is_a: core field
    slot_uri: MIXS:0000173
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  biomass:
    name: biomass
    annotations:
      expected_value:
        tag: expected_value
        value: biomass type;measurement value
      preferred_unit:
        tag: preferred_unit
        value: ton, kilogram, gram
      occurrence:
        tag: occurrence
        value: m
    description: Amount of biomass; should include the name for the part of biomass
      measured, e.g. Microbial, total. Can include multiple measurements
    title: biomass
    examples:
    - value: total;20 gram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - biomass
    rank: 6
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000174
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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]+)$
  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
    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
  bishomohopanol:
    name: bishomohopanol
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, microgram per gram
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of bishomohopanol
    title: bishomohopanol
    examples:
    - value: 14 microgram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - bishomohopanol
    rank: 7
    is_a: core field
    slot_uri: MIXS:0000175
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  bromide:
    name: bromide
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of bromide
    title: bromide
    examples:
    - value: 0.05 parts per million
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - bromide
    rank: 8
    is_a: core field
    slot_uri: MIXS:0000176
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  calcium:
    name: calcium
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter, micromole per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of calcium in the sample
    title: calcium
    examples:
    - value: 0.2 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - calcium
    rank: 9
    is_a: core field
    slot_uri: MIXS:0000432
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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)?)?)?)?$
  chloride:
    name: chloride
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of chloride in the sample
    title: chloride
    examples:
    - value: 5000 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chloride
    rank: 10
    is_a: core field
    slot_uri: MIXS:0000429
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  chlorophyll:
    name: chlorophyll
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per cubic meter, microgram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of chlorophyll
    title: chlorophyll
    examples:
    - value: 5 milligram per cubic meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chlorophyll
    rank: 11
    is_a: core field
    slot_uri: MIXS:0000177
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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.
    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
    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?$)):([0-5]\d)(:([0-5]\d))?$
  density:
    name: density
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram per cubic meter, gram per cubic centimeter
      occurrence:
        tag: occurrence
        value: '1'
    description: Density of the sample, which is its mass per unit volume (aka volumetric
      mass density)
    title: density
    examples:
    - value: 1000 kilogram per cubic meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - density
    rank: 12
    is_a: core field
    slot_uri: MIXS:0000435
    owner: Biosample
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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]+)?$
  diether_lipids:
    name: diether_lipids
    annotations:
      expected_value:
        tag: expected_value
        value: diether lipid name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: nanogram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of diether lipids; can include multiple types of diether
      lipids
    title: diether lipids
    examples:
    - value: 0.2 nanogram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - diether lipids
    rank: 13
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000178
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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]+)$
  diss_carb_dioxide:
    name: diss_carb_dioxide
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of dissolved carbon dioxide in the sample or liquid
      portion of the sample
    title: dissolved carbon dioxide
    examples:
    - value: 5 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved carbon dioxide
    rank: 14
    is_a: core field
    slot_uri: MIXS:0000436
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_hydrogen:
    name: diss_hydrogen
    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 dissolved hydrogen
    title: dissolved hydrogen
    examples:
    - value: 0.3 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved hydrogen
    rank: 15
    is_a: core field
    slot_uri: MIXS:0000179
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_inorg_carb:
    name: diss_inorg_carb
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Dissolved inorganic carbon concentration in the sample, typically
      measured after filtering the sample using a 0.45 micrometer filter
    title: dissolved inorganic carbon
    examples:
    - value: 2059 micromole per kilogram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved inorganic carbon
    rank: 16
    is_a: core field
    slot_uri: MIXS:0000434
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_org_carb:
    name: diss_org_carb
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of dissolved organic carbon in the sample, liquid portion
      of the sample, or aqueous phase of the fluid
    title: dissolved organic carbon
    examples:
    - value: 197 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved organic carbon
    rank: 17
    is_a: core field
    slot_uri: MIXS:0000433
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_org_nitro:
    name: diss_org_nitro
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Dissolved organic nitrogen concentration measured as; total dissolved
      nitrogen - NH4 - NO3 - NO2
    title: dissolved organic nitrogen
    examples:
    - value: 0.05 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved organic nitrogen
    rank: 18
    is_a: core field
    slot_uri: MIXS:0000162
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_oxygen:
    name: diss_oxygen
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per kilogram, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of dissolved oxygen
    title: dissolved oxygen
    examples:
    - value: 175 micromole per kilogram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved oxygen
    rank: 19
    is_a: core field
    slot_uri: MIXS:0000119
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: EcosystemEnum
    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: EcosystemCategoryEnum
    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: EcosystemSubtypeEnum
    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: EcosystemTypeEnum
    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
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  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
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  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
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  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: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
  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
    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
  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?
    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?
    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
    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
    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: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  glucosidase_act:
    name: glucosidase_act
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mol per liter per hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of glucosidase activity
    title: glucosidase activity
    examples:
    - value: 5 mol per liter per hour
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - glucosidase activity
    rank: 20
    is_a: core field
    slot_uri: MIXS:0000137
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
    multivalued: false
  isotope_exposure:
    name: isotope_exposure
    description: List isotope exposure or addition applied to your sample.
    title: isotope exposure/addition
    todos:
    - Can we make the H218O correctly super and subscripted?
    comments:
    - This is required when your experimental design includes the use of isotopically
      labeled compounds
    examples:
    - value: 13C glucose
    - value: H218O
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000751
    rank: 16
    string_serialization: '{termLabel} {[termID]}; {timestamp}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
  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})?)$
  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
    multivalued: false
    pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      \S+$
  magnesium:
    name: magnesium
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per liter, milligram per liter, parts per million, micromole per
          kilogram
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of magnesium in the sample
    title: magnesium
    examples:
    - value: 52.8 micromole per kilogram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - magnesium
    rank: 21
    is_a: core field
    slot_uri: MIXS:0000431
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  mean_frict_vel:
    name: mean_frict_vel
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: meter per second
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of mean friction velocity
    title: mean friction velocity
    examples:
    - value: 0.5 meter per second
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean friction velocity
    rank: 22
    is_a: core field
    slot_uri: MIXS:0000498
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  mean_peak_frict_vel:
    name: mean_peak_frict_vel
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: meter per second
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of mean peak friction velocity
    title: mean peak friction velocity
    examples:
    - value: 1 meter per second
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean peak friction velocity
    rank: 23
    is_a: core field
    slot_uri: MIXS:0000502
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  methane:
    name: methane
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter, parts per billion, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Methane (gas) amount or concentration at the time of sampling
    title: methane
    examples:
    - value: 1800 parts per billion
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - methane
    rank: 24
    is_a: core field
    slot_uri: MIXS:0000101
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - SedimentInterface
    slot_group: mixs_core_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]+)$
  n_alkanes:
    name: n_alkanes
    annotations:
      expected_value:
        tag: expected_value
        value: n-alkane name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of n-alkanes; can include multiple n-alkanes
    title: n-alkanes
    examples:
    - value: n-hexadecane;100 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - n-alkanes
    rank: 25
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000503
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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:
    name: nitrate
    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: Concentration of nitrate in the sample
    title: nitrate
    examples:
    - value: 65 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - nitrate
    rank: 26
    is_a: core field
    slot_uri: MIXS:0000425
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  nitrite:
    name: nitrite
    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: Concentration of nitrite in the sample
    title: nitrite
    examples:
    - value: 0.5 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - nitrite
    rank: 27
    is_a: core field
    slot_uri: MIXS:0000426
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  nitro:
    name: nitro
    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 nitrogen (total)
    title: nitrogen
    examples:
    - value: 4.2 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - nitrogen
    rank: 28
    is_a: core field
    slot_uri: MIXS:0000504
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  org_carb:
    name: org_carb
    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 organic carbon
    title: organic carbon
    examples:
    - value: 1.5 microgram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organic carbon
    rank: 29
    is_a: core field
    slot_uri: MIXS:0000508
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
  organism_count:
    name: organism_count
    annotations:
      expected_value:
        tag: expected_value
        value: organism name;measurement value;enumeration
      preferred_unit:
        tag: preferred_unit
        value: number of cells per cubic meter, number of cells per milliliter, number
          of cells per cubic centimeter
      occurrence:
        tag: occurrence
        value: m
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organism count
    rank: 30
    is_a: core field
    slot_uri: MIXS:0000103
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$
  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
  part_org_carb:
    name: part_org_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: Concentration of particulate organic carbon
    title: particulate organic carbon
    examples:
    - value: 1.92 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - particulate organic carbon
    rank: 31
    is_a: core field
    slot_uri: MIXS:0000515
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  particle_class:
    name: particle_class
    annotations:
      expected_value:
        tag: expected_value
        value: particle name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: micrometer
      occurrence:
        tag: occurrence
        value: m
    description: Particles are classified, based on their size, into six general categories:clay,
      silt, sand, gravel, cobbles, and boulders; should include amount of particle
      preceded by the name of the particle type; can include multiple values
    title: particle classification
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - particle classification
    rank: 32
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000206
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    slot_group: mixs_core_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]+)$
  perturbation:
    name: perturbation
    annotations:
      expected_value:
        tag: expected_value
        value: perturbation type name;perturbation interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Type of perturbation, e.g. chemical administration, physical disturbance,
      etc., coupled with perturbation regimen including how many times the perturbation
      was repeated, how long each perturbation lasted, and the start and end time
      of the entire perturbation period; can include multiple perturbation types
    title: perturbation
    examples:
    - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - perturbation
    rank: 33
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000754
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  petroleum_hydrocarb:
    name: petroleum_hydrocarb
    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 petroleum hydrocarbon
    title: petroleum hydrocarbon
    examples:
    - value: 0.05 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - petroleum hydrocarbon
    rank: 34
    is_a: core field
    slot_uri: MIXS:0000516
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
  phaeopigments:
    name: phaeopigments
    annotations:
      expected_value:
        tag: expected_value
        value: phaeopigment name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per cubic meter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of phaeopigments; can include multiple phaeopigments
    title: phaeopigments
    examples:
    - value: 2.5 milligram per cubic meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - phaeopigments
    rank: 35
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000180
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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]+)$
  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.*$
  phosplipid_fatt_acid:
    name: phosplipid_fatt_acid
    annotations:
      expected_value:
        tag: expected_value
        value: phospholipid fatty acid name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per gram, mole per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of phospholipid fatty acids; can include multiple values
    title: phospholipid fatty acid
    examples:
    - value: 2.98 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - phospholipid fatty acid
    rank: 36
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000181
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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]+)$
  porosity:
    name: porosity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value or range
      preferred_unit:
        tag: preferred_unit
        value: percentage
      occurrence:
        tag: occurrence
        value: '1'
    description: Porosity of deposited sediment is volume of voids divided by the
      total volume of sample
    title: porosity
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - porosity
    rank: 37
    is_a: core field
    string_serialization: '{float} - {float} {unit}'
    slot_uri: MIXS:0000211
    owner: Biosample
    domain_of:
    - Biosample
    - HcrCoresInterface
    - SedimentInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  potassium:
    name: potassium
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of potassium in the sample
    title: potassium
    examples:
    - value: 463 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - potassium
    rank: 38
    is_a: core field
    slot_uri: MIXS:0000430
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  pressure:
    name: pressure
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: atmosphere
      occurrence:
        tag: occurrence
        value: '1'
    description: Pressure to which the sample is subject to, in atmospheres
    title: pressure
    examples:
    - value: 50 atmosphere
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pressure
    rank: 39
    is_a: core field
    slot_uri: MIXS:0000412
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  redox_potential:
    name: redox_potential
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millivolt
      occurrence:
        tag: occurrence
        value: '1'
    description: Redox potential, measured relative to a hydrogen cell, indicating
      oxidation or reduction potential
    title: redox potential
    examples:
    - value: 300 millivolt
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - redox potential
    rank: 40
    is_a: core field
    slot_uri: MIXS:0000182
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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_dur:
    name: samp_store_dur
    annotations:
      expected_value:
        tag: expected_value
        value: duration
      occurrence:
        tag: occurrence
        value: '1'
    description: Duration for which the sample was stored
    title: sample storage duration
    examples:
    - value: P1Y6M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample storage duration
    rank: 353
    is_a: core field
    string_serialization: '{duration}'
    slot_uri: MIXS:0000116
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  samp_store_loc:
    name: samp_store_loc
    annotations:
      expected_value:
        tag: expected_value
        value: location name
      occurrence:
        tag: occurrence
        value: '1'
    description: Location at which sample was stored, usually name of a specific freezer/room
    title: sample storage location
    examples:
    - value: Freezer no:5
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample storage location
    rank: 41
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000755
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  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]+'
  sediment_type:
    name: sediment_type
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about the sediment type based on major constituents
    title: sediment type
    examples:
    - value: biogenous
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sediment type
    rank: 42
    is_a: core field
    slot_uri: MIXS:0001078
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    slot_group: mixs_core_section
    range: sediment_type_enum
    multivalued: false
  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
    comments:
    - Describe how samples were composited or sieved.
    - Use 'sample link' to indicate which samples were combined.
    examples:
    - value: combined 2 cores | 4mm sieved
    - value: 4 mm sieved and homogenized
    - value: 50 g | 5 cores | 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
    multivalued: false
  silicate:
    name: silicate
    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 silicate
    title: silicate
    examples:
    - value: 0.05 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - silicate
    rank: 43
    is_a: core field
    slot_uri: MIXS:0000184
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  size_frac:
    name: size_frac
    annotations:
      expected_value:
        tag: expected_value
        value: filter size value range
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    examples:
    - value: 0-0.22 micrometer
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - size fraction selected
    rank: 285
    is_a: nucleic acid sequence source field
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  sodium:
    name: sodium
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Sodium concentration in the sample
    title: sodium
    examples:
    - value: 10.5 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sodium
    rank: 363
    is_a: core field
    slot_uri: MIXS:0000428
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: SpecificEcosystemEnum
    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]))?)?$
  sulfate:
    name: sulfate
    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: Concentration of sulfate in the sample
    title: sulfate
    examples:
    - value: 5 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sulfate
    rank: 44
    is_a: core field
    slot_uri: MIXS:0000423
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  sulfide:
    name: sulfide
    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: Concentration of sulfide in the sample
    title: sulfide
    examples:
    - value: 2 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sulfide
    rank: 371
    is_a: core field
    slot_uri: MIXS:0000424
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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.*$
  tidal_stage:
    name: tidal_stage
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Stage of tide
    title: tidal stage
    examples:
    - value: high tide
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - tidal stage
    rank: 45
    is_a: core field
    slot_uri: MIXS:0000750
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: tidal_stage_enum
    multivalued: false
  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_depth_water_col:
    name: tot_depth_water_col
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: meter
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of total depth of water column
    title: total depth of water column
    examples:
    - value: 500 meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total depth of water column
    rank: 46
    is_a: core field
    slot_uri: MIXS:0000634
    owner: Biosample
    domain_of:
    - Biosample
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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.*$
  turbidity:
    name: turbidity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: formazin turbidity unit, formazin nephelometric units
      occurrence:
        tag: occurrence
        value: '1'
    description: Measure of the amount of cloudiness or haziness in water caused by
      individual particles
    title: turbidity
    examples:
    - value: 0.3 nephelometric turbidity units
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - turbidity
    rank: 47
    is_a: core field
    slot_uri: MIXS:0000191
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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?
    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
    multivalued: false
  horizon_meth:
    name: horizon_meth
    title: horizon method
attributes:
  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: SedimentInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
  alkalinity:
    name: alkalinity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milliequivalent per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Alkalinity, the ability of a solution to neutralize acids to the
      equivalence point of carbonate or bicarbonate
    title: alkalinity
    examples:
    - value: 50 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - alkalinity
    rank: 1
    is_a: core field
    slot_uri: MIXS:0000421
    alias: alkalinity
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  alkalinity_method:
    name: alkalinity_method
    annotations:
      expected_value:
        tag: expected_value
        value: description of method
      occurrence:
        tag: occurrence
        value: '1'
    description: Method used for alkalinity measurement
    title: alkalinity method
    examples:
    - value: titration
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - alkalinity method
    rank: 218
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000298
    alias: alkalinity_method
    owner: SedimentInterface
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  alkyl_diethers:
    name: alkyl_diethers
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of alkyl diethers
    title: alkyl diethers
    examples:
    - value: 0.005 mole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - alkyl diethers
    rank: 2
    is_a: core field
    slot_uri: MIXS:0000490
    alias: alkyl_diethers
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  aminopept_act:
    name: aminopept_act
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per liter per hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of aminopeptidase activity
    title: aminopeptidase activity
    examples:
    - value: 0.269 mole per liter per hour
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - aminopeptidase activity
    rank: 3
    is_a: core field
    slot_uri: MIXS:0000172
    alias: aminopept_act
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  ammonium:
    name: ammonium
    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: Concentration of ammonium in the sample
    title: ammonium
    examples:
    - value: 1.5 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - ammonium
    rank: 4
    is_a: core field
    slot_uri: MIXS:0000427
    alias: ammonium
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  bacteria_carb_prod:
    name: bacteria_carb_prod
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: nanogram per hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of bacterial carbon production
    title: bacterial carbon production
    examples:
    - value: 2.53 microgram per liter per hour
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - bacterial carbon production
    rank: 5
    is_a: core field
    slot_uri: MIXS:0000173
    alias: bacteria_carb_prod
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  biomass:
    name: biomass
    annotations:
      expected_value:
        tag: expected_value
        value: biomass type;measurement value
      preferred_unit:
        tag: preferred_unit
        value: ton, kilogram, gram
      occurrence:
        tag: occurrence
        value: m
    description: Amount of biomass; should include the name for the part of biomass
      measured, e.g. Microbial, total. Can include multiple measurements
    title: biomass
    examples:
    - value: total;20 gram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - biomass
    rank: 6
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000174
    alias: biomass
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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]+)$
  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: SedimentInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    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: SedimentInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: biotic_relationship_enum
    multivalued: false
  bishomohopanol:
    name: bishomohopanol
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, microgram per gram
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of bishomohopanol
    title: bishomohopanol
    examples:
    - value: 14 microgram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - bishomohopanol
    rank: 7
    is_a: core field
    slot_uri: MIXS:0000175
    alias: bishomohopanol
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  bromide:
    name: bromide
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of bromide
    title: bromide
    examples:
    - value: 0.05 parts per million
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - bromide
    rank: 8
    is_a: core field
    slot_uri: MIXS:0000176
    alias: bromide
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  calcium:
    name: calcium
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter, micromole per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of calcium in the sample
    title: calcium
    examples:
    - value: 0.2 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - calcium
    rank: 9
    is_a: core field
    slot_uri: MIXS:0000432
    alias: calcium
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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: SedimentInterface
    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: SedimentInterface
    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)?)?)?)?$
  chloride:
    name: chloride
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of chloride in the sample
    title: chloride
    examples:
    - value: 5000 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chloride
    rank: 10
    is_a: core field
    slot_uri: MIXS:0000429
    alias: chloride
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  chlorophyll:
    name: chlorophyll
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per cubic meter, microgram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of chlorophyll
    title: chlorophyll
    examples:
    - value: 5 milligram per cubic meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chlorophyll
    rank: 11
    is_a: core field
    slot_uri: MIXS:0000177
    alias: chlorophyll
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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.
    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: SedimentInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    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?$)):([0-5]\d)(:([0-5]\d))?$
  density:
    name: density
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram per cubic meter, gram per cubic centimeter
      occurrence:
        tag: occurrence
        value: '1'
    description: Density of the sample, which is its mass per unit volume (aka volumetric
      mass density)
    title: density
    examples:
    - value: 1000 kilogram per cubic meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - density
    rank: 12
    is_a: core field
    slot_uri: MIXS:0000435
    alias: density
    owner: SedimentInterface
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: SedimentInterface
    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]+)?$
  diether_lipids:
    name: diether_lipids
    annotations:
      expected_value:
        tag: expected_value
        value: diether lipid name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: nanogram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of diether lipids; can include multiple types of diether
      lipids
    title: diether lipids
    examples:
    - value: 0.2 nanogram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - diether lipids
    rank: 13
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000178
    alias: diether_lipids
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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]+)$
  diss_carb_dioxide:
    name: diss_carb_dioxide
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of dissolved carbon dioxide in the sample or liquid
      portion of the sample
    title: dissolved carbon dioxide
    examples:
    - value: 5 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved carbon dioxide
    rank: 14
    is_a: core field
    slot_uri: MIXS:0000436
    alias: diss_carb_dioxide
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_hydrogen:
    name: diss_hydrogen
    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 dissolved hydrogen
    title: dissolved hydrogen
    examples:
    - value: 0.3 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved hydrogen
    rank: 15
    is_a: core field
    slot_uri: MIXS:0000179
    alias: diss_hydrogen
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_inorg_carb:
    name: diss_inorg_carb
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Dissolved inorganic carbon concentration in the sample, typically
      measured after filtering the sample using a 0.45 micrometer filter
    title: dissolved inorganic carbon
    examples:
    - value: 2059 micromole per kilogram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved inorganic carbon
    rank: 16
    is_a: core field
    slot_uri: MIXS:0000434
    alias: diss_inorg_carb
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_org_carb:
    name: diss_org_carb
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of dissolved organic carbon in the sample, liquid portion
      of the sample, or aqueous phase of the fluid
    title: dissolved organic carbon
    examples:
    - value: 197 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved organic carbon
    rank: 17
    is_a: core field
    slot_uri: MIXS:0000433
    alias: diss_org_carb
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_org_nitro:
    name: diss_org_nitro
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Dissolved organic nitrogen concentration measured as; total dissolved
      nitrogen - NH4 - NO3 - NO2
    title: dissolved organic nitrogen
    examples:
    - value: 0.05 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved organic nitrogen
    rank: 18
    is_a: core field
    slot_uri: MIXS:0000162
    alias: diss_org_nitro
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  diss_oxygen:
    name: diss_oxygen
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per kilogram, milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of dissolved oxygen
    title: dissolved oxygen
    examples:
    - value: 175 micromole per kilogram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - dissolved oxygen
    rank: 19
    is_a: core field
    slot_uri: MIXS:0000119
    alias: diss_oxygen
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: SedimentInterface
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemEnum
    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: SedimentInterface
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemCategoryEnum
    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: SedimentInterface
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemSubtypeEnum
    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: SedimentInterface
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemTypeEnum
    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: SedimentInterface
    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: SedimentInterface
    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+ \[[a-zA-Z]{2,}:\d+\]$
  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: SedimentInterface
    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+ \[[a-zA-Z]{2,}:\d+\]$
  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: SedimentInterface
    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+ \[[a-zA-Z]{2,}:\d+\]$
  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: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: SedimentInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    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
    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: SedimentInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    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?
    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: SedimentInterface
    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?
    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: SedimentInterface
    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
    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: SedimentInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    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: SedimentInterface
    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: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  glucosidase_act:
    name: glucosidase_act
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mol per liter per hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of glucosidase activity
    title: glucosidase activity
    examples:
    - value: 5 mol per liter per hour
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - glucosidase activity
    rank: 20
    is_a: core field
    slot_uri: MIXS:0000137
    alias: glucosidase_act
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: SedimentInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
  isotope_exposure:
    name: isotope_exposure
    description: List isotope exposure or addition applied to your sample.
    title: isotope exposure/addition
    todos:
    - Can we make the H218O correctly super and subscripted?
    comments:
    - This is required when your experimental design includes the use of isotopically
      labeled compounds
    examples:
    - value: 13C glucose
    - value: H218O
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000751
    rank: 16
    string_serialization: '{termLabel} {[termID]}; {timestamp}'
    alias: isotope_exposure
    owner: SedimentInterface
    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: SedimentInterface
    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})?)$
  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: SedimentInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
    pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      \S+$
  magnesium:
    name: magnesium
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per liter, milligram per liter, parts per million, micromole per
          kilogram
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of magnesium in the sample
    title: magnesium
    examples:
    - value: 52.8 micromole per kilogram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - magnesium
    rank: 21
    is_a: core field
    slot_uri: MIXS:0000431
    alias: magnesium
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  mean_frict_vel:
    name: mean_frict_vel
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: meter per second
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of mean friction velocity
    title: mean friction velocity
    examples:
    - value: 0.5 meter per second
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean friction velocity
    rank: 22
    is_a: core field
    slot_uri: MIXS:0000498
    alias: mean_frict_vel
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  mean_peak_frict_vel:
    name: mean_peak_frict_vel
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: meter per second
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of mean peak friction velocity
    title: mean peak friction velocity
    examples:
    - value: 1 meter per second
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mean peak friction velocity
    rank: 23
    is_a: core field
    slot_uri: MIXS:0000502
    alias: mean_peak_frict_vel
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  methane:
    name: methane
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter, parts per billion, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Methane (gas) amount or concentration at the time of sampling
    title: methane
    examples:
    - value: 1800 parts per billion
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - methane
    rank: 24
    is_a: core field
    slot_uri: MIXS:0000101
    alias: methane
    owner: SedimentInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - SedimentInterface
    slot_group: mixs_core_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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    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]+)$
  n_alkanes:
    name: n_alkanes
    annotations:
      expected_value:
        tag: expected_value
        value: n-alkane name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of n-alkanes; can include multiple n-alkanes
    title: n-alkanes
    examples:
    - value: n-hexadecane;100 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - n-alkanes
    rank: 25
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000503
    alias: n_alkanes
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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:
    name: nitrate
    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: Concentration of nitrate in the sample
    title: nitrate
    examples:
    - value: 65 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - nitrate
    rank: 26
    is_a: core field
    slot_uri: MIXS:0000425
    alias: nitrate
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  nitrite:
    name: nitrite
    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: Concentration of nitrite in the sample
    title: nitrite
    examples:
    - value: 0.5 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - nitrite
    rank: 27
    is_a: core field
    slot_uri: MIXS:0000426
    alias: nitrite
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  nitro:
    name: nitro
    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 nitrogen (total)
    title: nitrogen
    examples:
    - value: 4.2 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - nitrogen
    rank: 28
    is_a: core field
    slot_uri: MIXS:0000504
    alias: nitro
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  org_carb:
    name: org_carb
    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 organic carbon
    title: organic carbon
    examples:
    - value: 1.5 microgram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organic carbon
    rank: 29
    is_a: core field
    slot_uri: MIXS:0000508
    alias: org_carb
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    multivalued: false
  organism_count:
    name: organism_count
    annotations:
      expected_value:
        tag: expected_value
        value: organism name;measurement value;enumeration
      preferred_unit:
        tag: preferred_unit
        value: number of cells per cubic meter, number of cells per milliliter, number
          of cells per cubic centimeter
      occurrence:
        tag: occurrence
        value: m
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organism count
    rank: 30
    is_a: core field
    slot_uri: MIXS:0000103
    alias: organism_count
    owner: SedimentInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$
  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: SedimentInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: OxyStatSampEnum
    multivalued: false
  part_org_carb:
    name: part_org_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: Concentration of particulate organic carbon
    title: particulate organic carbon
    examples:
    - value: 1.92 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - particulate organic carbon
    rank: 31
    is_a: core field
    slot_uri: MIXS:0000515
    alias: part_org_carb
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  particle_class:
    name: particle_class
    annotations:
      expected_value:
        tag: expected_value
        value: particle name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: micrometer
      occurrence:
        tag: occurrence
        value: m
    description: Particles are classified, based on their size, into six general categories:clay,
      silt, sand, gravel, cobbles, and boulders; should include amount of particle
      preceded by the name of the particle type; can include multiple values
    title: particle classification
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - particle classification
    rank: 32
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000206
    alias: particle_class
    owner: SedimentInterface
    domain_of:
    - Biosample
    - SedimentInterface
    slot_group: mixs_core_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]+)$
  perturbation:
    name: perturbation
    annotations:
      expected_value:
        tag: expected_value
        value: perturbation type name;perturbation interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Type of perturbation, e.g. chemical administration, physical disturbance,
      etc., coupled with perturbation regimen including how many times the perturbation
      was repeated, how long each perturbation lasted, and the start and end time
      of the entire perturbation period; can include multiple perturbation types
    title: perturbation
    examples:
    - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - perturbation
    rank: 33
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000754
    alias: perturbation
    owner: SedimentInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  petroleum_hydrocarb:
    name: petroleum_hydrocarb
    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 petroleum hydrocarbon
    title: petroleum hydrocarbon
    examples:
    - value: 0.05 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - petroleum hydrocarbon
    rank: 34
    is_a: core field
    slot_uri: MIXS:0000516
    alias: petroleum_hydrocarb
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: SedimentInterface
    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: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  phaeopigments:
    name: phaeopigments
    annotations:
      expected_value:
        tag: expected_value
        value: phaeopigment name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per cubic meter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of phaeopigments; can include multiple phaeopigments
    title: phaeopigments
    examples:
    - value: 2.5 milligram per cubic meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - phaeopigments
    rank: 35
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000180
    alias: phaeopigments
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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]+)$
  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: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  phosplipid_fatt_acid:
    name: phosplipid_fatt_acid
    annotations:
      expected_value:
        tag: expected_value
        value: phospholipid fatty acid name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per gram, mole per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of phospholipid fatty acids; can include multiple values
    title: phospholipid fatty acid
    examples:
    - value: 2.98 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - phospholipid fatty acid
    rank: 36
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000181
    alias: phosplipid_fatt_acid
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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]+)$
  porosity:
    name: porosity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value or range
      preferred_unit:
        tag: preferred_unit
        value: percentage
      occurrence:
        tag: occurrence
        value: '1'
    description: Porosity of deposited sediment is volume of voids divided by the
      total volume of sample
    title: porosity
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - porosity
    rank: 37
    is_a: core field
    string_serialization: '{float} - {float} {unit}'
    slot_uri: MIXS:0000211
    alias: porosity
    owner: SedimentInterface
    domain_of:
    - Biosample
    - HcrCoresInterface
    - SedimentInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  potassium:
    name: potassium
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of potassium in the sample
    title: potassium
    examples:
    - value: 463 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - potassium
    rank: 38
    is_a: core field
    slot_uri: MIXS:0000430
    alias: potassium
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  pressure:
    name: pressure
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: atmosphere
      occurrence:
        tag: occurrence
        value: '1'
    description: Pressure to which the sample is subject to, in atmospheres
    title: pressure
    examples:
    - value: 50 atmosphere
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pressure
    rank: 39
    is_a: core field
    slot_uri: MIXS:0000412
    alias: pressure
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  redox_potential:
    name: redox_potential
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millivolt
      occurrence:
        tag: occurrence
        value: '1'
    description: Redox potential, measured relative to a hydrogen cell, indicating
      oxidation or reduction potential
    title: redox potential
    examples:
    - value: 300 millivolt
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - redox potential
    rank: 40
    is_a: core field
    slot_uri: MIXS:0000182
    alias: redox_potential
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    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_dur:
    name: samp_store_dur
    annotations:
      expected_value:
        tag: expected_value
        value: duration
      occurrence:
        tag: occurrence
        value: '1'
    description: Duration for which the sample was stored
    title: sample storage duration
    examples:
    - value: P1Y6M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample storage duration
    rank: 353
    is_a: core field
    string_serialization: '{duration}'
    slot_uri: MIXS:0000116
    alias: samp_store_dur
    owner: SedimentInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  samp_store_loc:
    name: samp_store_loc
    annotations:
      expected_value:
        tag: expected_value
        value: location name
      occurrence:
        tag: occurrence
        value: '1'
    description: Location at which sample was stored, usually name of a specific freezer/room
    title: sample storage location
    examples:
    - value: Freezer no:5
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample storage location
    rank: 41
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000755
    alias: samp_store_loc
    owner: SedimentInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  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: SedimentInterface
    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: SedimentInterface
    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]+'
  sediment_type:
    name: sediment_type
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about the sediment type based on major constituents
    title: sediment type
    examples:
    - value: biogenous
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sediment type
    rank: 42
    is_a: core field
    slot_uri: MIXS:0001078
    alias: sediment_type
    owner: SedimentInterface
    domain_of:
    - Biosample
    - SedimentInterface
    slot_group: mixs_core_section
    range: sediment_type_enum
    multivalued: false
  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
    comments:
    - Describe how samples were composited or sieved.
    - Use 'sample link' to indicate which samples were combined.
    examples:
    - value: combined 2 cores | 4mm sieved
    - value: 4 mm sieved and homogenized
    - value: 50 g | 5 cores | 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: SedimentInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
  silicate:
    name: silicate
    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 silicate
    title: silicate
    examples:
    - value: 0.05 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - silicate
    rank: 43
    is_a: core field
    slot_uri: MIXS:0000184
    alias: silicate
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  size_frac:
    name: size_frac
    annotations:
      expected_value:
        tag: expected_value
        value: filter size value range
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    examples:
    - value: 0-0.22 micrometer
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - size fraction selected
    rank: 285
    is_a: nucleic acid sequence source field
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    alias: size_frac
    owner: SedimentInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  sodium:
    name: sodium
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter, parts per million
      occurrence:
        tag: occurrence
        value: '1'
    description: Sodium concentration in the sample
    title: sodium
    examples:
    - value: 10.5 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sodium
    rank: 363
    is_a: core field
    slot_uri: MIXS:0000428
    alias: sodium
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: SedimentInterface
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: SpecificEcosystemEnum
    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: SedimentInterface
    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]))?)?$
  sulfate:
    name: sulfate
    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: Concentration of sulfate in the sample
    title: sulfate
    examples:
    - value: 5 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sulfate
    rank: 44
    is_a: core field
    slot_uri: MIXS:0000423
    alias: sulfate
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  sulfide:
    name: sulfide
    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: Concentration of sulfide in the sample
    title: sulfide
    examples:
    - value: 2 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sulfide
    rank: 371
    is_a: core field
    slot_uri: MIXS:0000424
    alias: sulfide
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: SedimentInterface
    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.*$
  tidal_stage:
    name: tidal_stage
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Stage of tide
    title: tidal stage
    examples:
    - value: high tide
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - tidal stage
    rank: 45
    is_a: core field
    slot_uri: MIXS:0000750
    alias: tidal_stage
    owner: SedimentInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: tidal_stage_enum
    multivalued: false
  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: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tot_depth_water_col:
    name: tot_depth_water_col
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: meter
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of total depth of water column
    title: total depth of water column
    examples:
    - value: 500 meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total depth of water column
    rank: 46
    is_a: core field
    slot_uri: MIXS:0000634
    alias: tot_depth_water_col
    owner: SedimentInterface
    domain_of:
    - Biosample
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  turbidity:
    name: turbidity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: formazin turbidity unit, formazin nephelometric units
      occurrence:
        tag: occurrence
        value: '1'
    description: Measure of the amount of cloudiness or haziness in water caused by
      individual particles
    title: turbidity
    examples:
    - value: 0.3 nephelometric turbidity units
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - turbidity
    rank: 47
    is_a: core field
    slot_uri: MIXS:0000191
    alias: turbidity
    owner: SedimentInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - SedimentInterface
    - WaterInterface
    slot_group: mixs_core_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?
    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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
  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: SedimentInterface
    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: SedimentInterface
    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: SedimentInterface
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    multivalued: false
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'