Class: Wastewater Sludge (WastewaterSludgeInterface)

name: WastewaterSludgeInterface
annotations:
  excel_worksheet_name:
    tag: excel_worksheet_name
    value: wastewater sludge
description: wastewater_sludge dh_interface
title: Wastewater Sludge
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
- SampIdNewTermsMixin
slots:
- alkalinity
- biochem_oxygen_dem
- chem_administration
- chem_oxygen_dem
- collection_date
- depth
- ecosystem
- ecosystem_category
- ecosystem_subtype
- ecosystem_type
- efficiency_percent
- elev
- emulsions
- env_broad_scale
- env_local_scale
- env_medium
- experimental_factor
- gaseous_substances
- geo_loc_name
- indust_eff_percent
- inorg_particles
- lat_lon
- misc_param
- nitrate
- org_particles
- organism_count
- oxy_stat_samp
- perturbation
- ph
- ph_meth
- phosphate
- pre_treatment
- primary_treatment
- reactor_type
- salinity
- samp_collec_device
- samp_collec_method
- samp_mat_process
- samp_size
- samp_store_dur
- samp_store_loc
- samp_store_temp
- sample_link
- secondary_treatment
- sewage_type
- size_frac
- sludge_retent_time
- sodium
- soluble_inorg_mat
- soluble_org_mat
- specific_ecosystem
- suspend_solids
- temp
- tertiary_treatment
- tot_nitro
- tot_phosphate
- wastewater_type
slot_usage:
  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.*$
  biochem_oxygen_dem:
    name: biochem_oxygen_dem
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Amount of dissolved oxygen needed by aerobic biological organisms
      in a body of water to break down organic material present in a given water sample
      at certain temperature over a specific time period
    title: biochemical oxygen demand
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - biochemical oxygen demand
    rank: 296
    is_a: core field
    slot_uri: MIXS:0000653
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    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)?)?)?)?$
  chem_oxygen_dem:
    name: chem_oxygen_dem
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: A measure of the capacity of water to consume oxygen during the decomposition
      of organic matter and the oxidation of inorganic chemicals such as ammonia and
      nitrite
    title: chemical oxygen demand
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chemical oxygen demand
    rank: 301
    is_a: core field
    slot_uri: MIXS:0000656
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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]))?)?$
  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}-{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
    recommended: true
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?(\s*-\s*[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)?$
  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
  efficiency_percent:
    name: efficiency_percent
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Percentage of volatile solids removed from the anaerobic digestor
    title: efficiency percent
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - efficiency percent
    rank: 307
    is_a: core field
    slot_uri: MIXS:0000657
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
  emulsions:
    name: emulsions
    annotations:
      expected_value:
        tag: expected_value
        value: emulsion name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Amount or concentration of substances such as paints, adhesives,
      mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion
      types
    title: emulsions
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - emulsions
    rank: 308
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000660
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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
  gaseous_substances:
    name: gaseous_substances
    annotations:
      expected_value:
        tag: expected_value
        value: gaseous substance name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: m
    description: Amount or concentration of substances such as hydrogen sulfide, carbon
      dioxide, methane, etc.; can include multiple substances
    title: gaseous substances
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gaseous substances
    rank: 311
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000661
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  indust_eff_percent:
    name: indust_eff_percent
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: percentage
      occurrence:
        tag: occurrence
        value: '1'
    description: Percentage of industrial effluents received by wastewater treatment
      plant
    title: industrial effluent percent
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - industrial effluent percent
    rank: 332
    is_a: core field
    slot_uri: MIXS:0000662
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  inorg_particles:
    name: inorg_particles
    annotations:
      expected_value:
        tag: expected_value
        value: inorganic particle name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of particles such as sand, grit, metal particles, ceramics,
      etc.; can include multiple particles
    title: inorganic particles
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - inorganic particles
    rank: 333
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000664
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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})?)$
  misc_param:
    name: misc_param
    annotations:
      expected_value:
        tag: expected_value
        value: parameter name;measurement value
      occurrence:
        tag: occurrence
        value: m
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    examples:
    - value: Bicarbonate ion concentration;2075 micromole per kilogram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - miscellaneous parameter
    rank: 23
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      [^;\t\r\x0A]+)$
  nitrate:
    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.*$
  org_particles:
    name: org_particles
    annotations:
      expected_value:
        tag: expected_value
        value: particle name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of particles such as faeces, hairs, food, vomit, paper
      fibers, plant material, humus, etc.
    title: organic particles
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organic particles
    rank: 338
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000665
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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
  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
  ph:
    name: ph
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    description: pH measurement of the sample, or liquid portion of sample, or aqueous
      phase of the fluid
    title: pH
    notes:
    - Use modified term
    examples:
    - value: '7.2'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pH
    rank: 27
    is_a: core field
    string_serialization: '{float}'
    slot_uri: MIXS:0001001
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: float
    recommended: true
    multivalued: false
    minimum_value: 0
    maximum_value: 14
  ph_meth:
    name: ph_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining ph
    title: pH method
    comments:
    - This can include a link to the instrument used or a citation for the method.
    examples:
    - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB
    - value: https://doi.org/10.2136/sssabookser5.3.c16
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pH method
    rank: 41
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0001106
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  phosphate:
    name: phosphate
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of phosphate
    title: phosphate
    examples:
    - value: 0.7 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - phosphate
    rank: 53
    is_a: core field
    slot_uri: MIXS:0000505
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  pre_treatment:
    name: pre_treatment
    annotations:
      expected_value:
        tag: expected_value
        value: pre-treatment type
      occurrence:
        tag: occurrence
        value: '1'
    description: The process of pre-treatment removes materials that can be easily
      collected from the raw wastewater
    title: pre-treatment
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pre-treatment
    rank: 342
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000348
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  primary_treatment:
    name: primary_treatment
    annotations:
      expected_value:
        tag: expected_value
        value: primary treatment type
      occurrence:
        tag: occurrence
        value: '1'
    description: The process to produce both a generally homogeneous liquid capable
      of being treated biologically and a sludge that can be separately treated or
      processed
    title: primary treatment
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - primary treatment
    rank: 343
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000349
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  reactor_type:
    name: reactor_type
    annotations:
      expected_value:
        tag: expected_value
        value: reactor type name
      occurrence:
        tag: occurrence
        value: '1'
    description: Anaerobic digesters can be designed and engineered to operate using
      a number of different process configurations, as batch or continuous, mesophilic,
      high solid or low solid, and single stage or multistage
    title: reactor type
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - reactor type
    rank: 346
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000350
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  salinity:
    name: salinity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: practical salinity unit, percentage
      occurrence:
        tag: occurrence
        value: '1'
    description: The total concentration of all dissolved salts in a liquid or solid
      sample. While salinity can be measured by a complete chemical analysis, this
      method is difficult and time consuming. More often, it is instead derived from
      the conductivity measurement. This is known as practical salinity. These derivations
      compare the specific conductance of the sample to a salinity standard such as
      seawater.
    title: salinity
    examples:
    - value: 25 practical salinity unit
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - salinity
    rank: 54
    is_a: core field
    slot_uri: MIXS:0000183
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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]+'
  secondary_treatment:
    name: secondary_treatment
    annotations:
      expected_value:
        tag: expected_value
        value: secondary treatment type
      occurrence:
        tag: occurrence
        value: '1'
    description: The process for substantially degrading the biological content of
      the sewage
    title: secondary treatment
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - secondary treatment
    rank: 360
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000351
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  sewage_type:
    name: sewage_type
    annotations:
      expected_value:
        tag: expected_value
        value: sewage type name
      occurrence:
        tag: occurrence
        value: '1'
    description: Type of wastewater treatment plant as municipial or industrial
    title: sewage type
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sewage type
    rank: 361
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000215
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  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
  sludge_retent_time:
    name: sludge_retent_time
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: hours
      occurrence:
        tag: occurrence
        value: '1'
    description: The time activated sludge remains in reactor
    title: sludge retention time
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sludge retention time
    rank: 362
    is_a: core field
    slot_uri: MIXS:0000669
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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.*$
  soluble_inorg_mat:
    name: soluble_inorg_mat
    annotations:
      expected_value:
        tag: expected_value
        value: soluble inorganic material name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram, microgram, mole per liter, gram per liter, parts per million
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of substances such as ammonia, road-salt, sea-salt,
      cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.
    title: soluble inorganic material
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soluble inorganic material
    rank: 364
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000672
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  soluble_org_mat:
    name: soluble_org_mat
    annotations:
      expected_value:
        tag: expected_value
        value: soluble organic material name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram, microgram, mole per liter, gram per liter, parts per million
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of substances such as urea, fruit sugars, soluble proteins,
      drugs, pharmaceuticals, etc.
    title: soluble organic material
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soluble organic material
    rank: 365
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000673
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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
  suspend_solids:
    name: suspend_solids
    annotations:
      expected_value:
        tag: expected_value
        value: suspended solid name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram, microgram, milligram per liter, mole per liter, gram per liter,
          part per million
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of substances including a wide variety of material,
      such as silt, decaying plant and animal matter; can include multiple substances
    title: suspended solids
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - suspended solids
    rank: 372
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000150
    owner: Biosample
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - WastewaterSludgeInterface
    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]+)$
  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.*$
  tertiary_treatment:
    name: tertiary_treatment
    annotations:
      expected_value:
        tag: expected_value
        value: tertiary treatment type
      occurrence:
        tag: occurrence
        value: '1'
    description: The process providing a final treatment stage to raise the effluent
      quality before it is discharged to the receiving environment
    title: tertiary treatment
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - tertiary treatment
    rank: 374
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000352
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  tot_nitro:
    name: tot_nitro
    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 concentration of water samples, calculated by: total
      nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured
      without filtering, reported as nitrogen'
    title: total nitrogen concentration
    examples:
    - value: 50 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total nitrogen concentration
    rank: 377
    is_a: core field
    slot_uri: MIXS:0000102
    owner: Biosample
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tot_phosphate:
    name: tot_phosphate
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, micromole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Total amount or concentration of phosphate
    title: total phosphate
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total phosphate
    rank: 378
    is_a: core field
    slot_uri: MIXS:0000689
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  wastewater_type:
    name: wastewater_type
    annotations:
      expected_value:
        tag: expected_value
        value: wastewater type name
      occurrence:
        tag: occurrence
        value: '1'
    description: The origin of wastewater such as human waste, rainfall, storm drains,
      etc.
    title: wastewater type
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - wastewater type
    rank: 385
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000353
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  horizon_meth:
    name: horizon_meth
    title: horizon method

name: WastewaterSludgeInterface
annotations:
  excel_worksheet_name:
    tag: excel_worksheet_name
    value: wastewater sludge
description: wastewater_sludge dh_interface
title: Wastewater Sludge
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
- SampIdNewTermsMixin
slot_usage:
  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.*$
  biochem_oxygen_dem:
    name: biochem_oxygen_dem
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Amount of dissolved oxygen needed by aerobic biological organisms
      in a body of water to break down organic material present in a given water sample
      at certain temperature over a specific time period
    title: biochemical oxygen demand
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - biochemical oxygen demand
    rank: 296
    is_a: core field
    slot_uri: MIXS:0000653
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    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)?)?)?)?$
  chem_oxygen_dem:
    name: chem_oxygen_dem
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: A measure of the capacity of water to consume oxygen during the decomposition
      of organic matter and the oxidation of inorganic chemicals such as ammonia and
      nitrite
    title: chemical oxygen demand
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chemical oxygen demand
    rank: 301
    is_a: core field
    slot_uri: MIXS:0000656
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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]))?)?$
  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}-{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
    recommended: true
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?(\s*-\s*[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)?$
  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
  efficiency_percent:
    name: efficiency_percent
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Percentage of volatile solids removed from the anaerobic digestor
    title: efficiency percent
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - efficiency percent
    rank: 307
    is_a: core field
    slot_uri: MIXS:0000657
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
  emulsions:
    name: emulsions
    annotations:
      expected_value:
        tag: expected_value
        value: emulsion name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Amount or concentration of substances such as paints, adhesives,
      mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion
      types
    title: emulsions
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - emulsions
    rank: 308
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000660
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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
  gaseous_substances:
    name: gaseous_substances
    annotations:
      expected_value:
        tag: expected_value
        value: gaseous substance name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: m
    description: Amount or concentration of substances such as hydrogen sulfide, carbon
      dioxide, methane, etc.; can include multiple substances
    title: gaseous substances
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gaseous substances
    rank: 311
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000661
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  indust_eff_percent:
    name: indust_eff_percent
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: percentage
      occurrence:
        tag: occurrence
        value: '1'
    description: Percentage of industrial effluents received by wastewater treatment
      plant
    title: industrial effluent percent
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - industrial effluent percent
    rank: 332
    is_a: core field
    slot_uri: MIXS:0000662
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  inorg_particles:
    name: inorg_particles
    annotations:
      expected_value:
        tag: expected_value
        value: inorganic particle name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of particles such as sand, grit, metal particles, ceramics,
      etc.; can include multiple particles
    title: inorganic particles
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - inorganic particles
    rank: 333
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000664
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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})?)$
  misc_param:
    name: misc_param
    annotations:
      expected_value:
        tag: expected_value
        value: parameter name;measurement value
      occurrence:
        tag: occurrence
        value: m
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    examples:
    - value: Bicarbonate ion concentration;2075 micromole per kilogram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - miscellaneous parameter
    rank: 23
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      [^;\t\r\x0A]+)$
  nitrate:
    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.*$
  org_particles:
    name: org_particles
    annotations:
      expected_value:
        tag: expected_value
        value: particle name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of particles such as faeces, hairs, food, vomit, paper
      fibers, plant material, humus, etc.
    title: organic particles
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organic particles
    rank: 338
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000665
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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
  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
  ph:
    name: ph
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    description: pH measurement of the sample, or liquid portion of sample, or aqueous
      phase of the fluid
    title: pH
    notes:
    - Use modified term
    examples:
    - value: '7.2'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pH
    rank: 27
    is_a: core field
    string_serialization: '{float}'
    slot_uri: MIXS:0001001
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: float
    recommended: true
    multivalued: false
    minimum_value: 0
    maximum_value: 14
  ph_meth:
    name: ph_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining ph
    title: pH method
    comments:
    - This can include a link to the instrument used or a citation for the method.
    examples:
    - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB
    - value: https://doi.org/10.2136/sssabookser5.3.c16
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pH method
    rank: 41
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0001106
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  phosphate:
    name: phosphate
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of phosphate
    title: phosphate
    examples:
    - value: 0.7 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - phosphate
    rank: 53
    is_a: core field
    slot_uri: MIXS:0000505
    owner: Biosample
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  pre_treatment:
    name: pre_treatment
    annotations:
      expected_value:
        tag: expected_value
        value: pre-treatment type
      occurrence:
        tag: occurrence
        value: '1'
    description: The process of pre-treatment removes materials that can be easily
      collected from the raw wastewater
    title: pre-treatment
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pre-treatment
    rank: 342
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000348
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  primary_treatment:
    name: primary_treatment
    annotations:
      expected_value:
        tag: expected_value
        value: primary treatment type
      occurrence:
        tag: occurrence
        value: '1'
    description: The process to produce both a generally homogeneous liquid capable
      of being treated biologically and a sludge that can be separately treated or
      processed
    title: primary treatment
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - primary treatment
    rank: 343
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000349
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  reactor_type:
    name: reactor_type
    annotations:
      expected_value:
        tag: expected_value
        value: reactor type name
      occurrence:
        tag: occurrence
        value: '1'
    description: Anaerobic digesters can be designed and engineered to operate using
      a number of different process configurations, as batch or continuous, mesophilic,
      high solid or low solid, and single stage or multistage
    title: reactor type
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - reactor type
    rank: 346
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000350
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  salinity:
    name: salinity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: practical salinity unit, percentage
      occurrence:
        tag: occurrence
        value: '1'
    description: The total concentration of all dissolved salts in a liquid or solid
      sample. While salinity can be measured by a complete chemical analysis, this
      method is difficult and time consuming. More often, it is instead derived from
      the conductivity measurement. This is known as practical salinity. These derivations
      compare the specific conductance of the sample to a salinity standard such as
      seawater.
    title: salinity
    examples:
    - value: 25 practical salinity unit
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - salinity
    rank: 54
    is_a: core field
    slot_uri: MIXS:0000183
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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]+'
  secondary_treatment:
    name: secondary_treatment
    annotations:
      expected_value:
        tag: expected_value
        value: secondary treatment type
      occurrence:
        tag: occurrence
        value: '1'
    description: The process for substantially degrading the biological content of
      the sewage
    title: secondary treatment
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - secondary treatment
    rank: 360
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000351
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  sewage_type:
    name: sewage_type
    annotations:
      expected_value:
        tag: expected_value
        value: sewage type name
      occurrence:
        tag: occurrence
        value: '1'
    description: Type of wastewater treatment plant as municipial or industrial
    title: sewage type
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sewage type
    rank: 361
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000215
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  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
  sludge_retent_time:
    name: sludge_retent_time
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: hours
      occurrence:
        tag: occurrence
        value: '1'
    description: The time activated sludge remains in reactor
    title: sludge retention time
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sludge retention time
    rank: 362
    is_a: core field
    slot_uri: MIXS:0000669
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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.*$
  soluble_inorg_mat:
    name: soluble_inorg_mat
    annotations:
      expected_value:
        tag: expected_value
        value: soluble inorganic material name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram, microgram, mole per liter, gram per liter, parts per million
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of substances such as ammonia, road-salt, sea-salt,
      cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.
    title: soluble inorganic material
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soluble inorganic material
    rank: 364
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000672
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  soluble_org_mat:
    name: soluble_org_mat
    annotations:
      expected_value:
        tag: expected_value
        value: soluble organic material name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram, microgram, mole per liter, gram per liter, parts per million
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of substances such as urea, fruit sugars, soluble proteins,
      drugs, pharmaceuticals, etc.
    title: soluble organic material
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soluble organic material
    rank: 365
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000673
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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
  suspend_solids:
    name: suspend_solids
    annotations:
      expected_value:
        tag: expected_value
        value: suspended solid name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram, microgram, milligram per liter, mole per liter, gram per liter,
          part per million
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of substances including a wide variety of material,
      such as silt, decaying plant and animal matter; can include multiple substances
    title: suspended solids
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - suspended solids
    rank: 372
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000150
    owner: Biosample
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - WastewaterSludgeInterface
    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]+)$
  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.*$
  tertiary_treatment:
    name: tertiary_treatment
    annotations:
      expected_value:
        tag: expected_value
        value: tertiary treatment type
      occurrence:
        tag: occurrence
        value: '1'
    description: The process providing a final treatment stage to raise the effluent
      quality before it is discharged to the receiving environment
    title: tertiary treatment
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - tertiary treatment
    rank: 374
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000352
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  tot_nitro:
    name: tot_nitro
    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 concentration of water samples, calculated by: total
      nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured
      without filtering, reported as nitrogen'
    title: total nitrogen concentration
    examples:
    - value: 50 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total nitrogen concentration
    rank: 377
    is_a: core field
    slot_uri: MIXS:0000102
    owner: Biosample
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tot_phosphate:
    name: tot_phosphate
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, micromole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Total amount or concentration of phosphate
    title: total phosphate
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total phosphate
    rank: 378
    is_a: core field
    slot_uri: MIXS:0000689
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  wastewater_type:
    name: wastewater_type
    annotations:
      expected_value:
        tag: expected_value
        value: wastewater type name
      occurrence:
        tag: occurrence
        value: '1'
    description: The origin of wastewater such as human waste, rainfall, storm drains,
      etc.
    title: wastewater type
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - wastewater type
    rank: 385
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000353
    owner: Biosample
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  horizon_meth:
    name: horizon_meth
    title: horizon method
attributes:
  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: WastewaterSludgeInterface
    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.*$
  biochem_oxygen_dem:
    name: biochem_oxygen_dem
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Amount of dissolved oxygen needed by aerobic biological organisms
      in a body of water to break down organic material present in a given water sample
      at certain temperature over a specific time period
    title: biochemical oxygen demand
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - biochemical oxygen demand
    rank: 296
    is_a: core field
    slot_uri: MIXS:0000653
    alias: biochem_oxygen_dem
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    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: WastewaterSludgeInterface
    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)?)?)?)?$
  chem_oxygen_dem:
    name: chem_oxygen_dem
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: A measure of the capacity of water to consume oxygen during the decomposition
      of organic matter and the oxidation of inorganic chemicals such as ammonia and
      nitrite
    title: chemical oxygen demand
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chemical oxygen demand
    rank: 301
    is_a: core field
    slot_uri: MIXS:0000656
    alias: chem_oxygen_dem
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: WastewaterSludgeInterface
    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]))?)?$
  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}-{float}'
    slot_uri: MIXS:0000018
    alias: depth
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?(\s*-\s*[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)?$
  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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    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
  efficiency_percent:
    name: efficiency_percent
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Percentage of volatile solids removed from the anaerobic digestor
    title: efficiency percent
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - efficiency percent
    rank: 307
    is_a: core field
    slot_uri: MIXS:0000657
    alias: efficiency_percent
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: WastewaterSludgeInterface
    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
  emulsions:
    name: emulsions
    annotations:
      expected_value:
        tag: expected_value
        value: emulsion name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Amount or concentration of substances such as paints, adhesives,
      mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion
      types
    title: emulsions
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - emulsions
    rank: 308
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000660
    alias: emulsions
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  gaseous_substances:
    name: gaseous_substances
    annotations:
      expected_value:
        tag: expected_value
        value: gaseous substance name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: m
    description: Amount or concentration of substances such as hydrogen sulfide, carbon
      dioxide, methane, etc.; can include multiple substances
    title: gaseous substances
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gaseous substances
    rank: 311
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000661
    alias: gaseous_substances
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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: WastewaterSludgeInterface
    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: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  indust_eff_percent:
    name: indust_eff_percent
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: percentage
      occurrence:
        tag: occurrence
        value: '1'
    description: Percentage of industrial effluents received by wastewater treatment
      plant
    title: industrial effluent percent
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - industrial effluent percent
    rank: 332
    is_a: core field
    slot_uri: MIXS:0000662
    alias: indust_eff_percent
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  inorg_particles:
    name: inorg_particles
    annotations:
      expected_value:
        tag: expected_value
        value: inorganic particle name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of particles such as sand, grit, metal particles, ceramics,
      etc.; can include multiple particles
    title: inorganic particles
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - inorganic particles
    rank: 333
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000664
    alias: inorg_particles
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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: WastewaterSludgeInterface
    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})?)$
  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: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      [^;\t\r\x0A]+)$
  nitrate:
    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: WastewaterSludgeInterface
    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.*$
  org_particles:
    name: org_particles
    annotations:
      expected_value:
        tag: expected_value
        value: particle name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of particles such as faeces, hairs, food, vomit, paper
      fibers, plant material, humus, etc.
    title: organic particles
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organic particles
    rank: 338
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000665
    alias: org_particles
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: OxyStatSampEnum
    multivalued: false
  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: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  ph:
    name: ph
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    description: pH measurement of the sample, or liquid portion of sample, or aqueous
      phase of the fluid
    title: pH
    notes:
    - Use modified term
    examples:
    - value: '7.2'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pH
    rank: 27
    is_a: core field
    string_serialization: '{float}'
    slot_uri: MIXS:0001001
    alias: ph
    owner: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  phosphate:
    name: phosphate
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Concentration of phosphate
    title: phosphate
    examples:
    - value: 0.7 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - phosphate
    rank: 53
    is_a: core field
    slot_uri: MIXS:0000505
    alias: phosphate
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - BiofilmInterface
    - MiscEnvsInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  pre_treatment:
    name: pre_treatment
    annotations:
      expected_value:
        tag: expected_value
        value: pre-treatment type
      occurrence:
        tag: occurrence
        value: '1'
    description: The process of pre-treatment removes materials that can be easily
      collected from the raw wastewater
    title: pre-treatment
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pre-treatment
    rank: 342
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000348
    alias: pre_treatment
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  primary_treatment:
    name: primary_treatment
    annotations:
      expected_value:
        tag: expected_value
        value: primary treatment type
      occurrence:
        tag: occurrence
        value: '1'
    description: The process to produce both a generally homogeneous liquid capable
      of being treated biologically and a sludge that can be separately treated or
      processed
    title: primary treatment
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - primary treatment
    rank: 343
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000349
    alias: primary_treatment
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  reactor_type:
    name: reactor_type
    annotations:
      expected_value:
        tag: expected_value
        value: reactor type name
      occurrence:
        tag: occurrence
        value: '1'
    description: Anaerobic digesters can be designed and engineered to operate using
      a number of different process configurations, as batch or continuous, mesophilic,
      high solid or low solid, and single stage or multistage
    title: reactor type
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - reactor type
    rank: 346
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000350
    alias: reactor_type
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  salinity:
    name: salinity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: practical salinity unit, percentage
      occurrence:
        tag: occurrence
        value: '1'
    description: The total concentration of all dissolved salts in a liquid or solid
      sample. While salinity can be measured by a complete chemical analysis, this
      method is difficult and time consuming. More often, it is instead derived from
      the conductivity measurement. This is known as practical salinity. These derivations
      compare the specific conductance of the sample to a salinity standard such as
      seawater.
    title: salinity
    examples:
    - value: 25 practical salinity unit
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - salinity
    rank: 54
    is_a: core field
    slot_uri: MIXS:0000183
    alias: salinity
    owner: WastewaterSludgeInterface
    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.*$
  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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    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]+'
  secondary_treatment:
    name: secondary_treatment
    annotations:
      expected_value:
        tag: expected_value
        value: secondary treatment type
      occurrence:
        tag: occurrence
        value: '1'
    description: The process for substantially degrading the biological content of
      the sewage
    title: secondary treatment
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - secondary treatment
    rank: 360
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000351
    alias: secondary_treatment
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  sewage_type:
    name: sewage_type
    annotations:
      expected_value:
        tag: expected_value
        value: sewage type name
      occurrence:
        tag: occurrence
        value: '1'
    description: Type of wastewater treatment plant as municipial or industrial
    title: sewage type
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sewage type
    rank: 361
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000215
    alias: sewage_type
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  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: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  sludge_retent_time:
    name: sludge_retent_time
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: hours
      occurrence:
        tag: occurrence
        value: '1'
    description: The time activated sludge remains in reactor
    title: sludge retention time
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sludge retention time
    rank: 362
    is_a: core field
    slot_uri: MIXS:0000669
    alias: sludge_retent_time
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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: WastewaterSludgeInterface
    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.*$
  soluble_inorg_mat:
    name: soluble_inorg_mat
    annotations:
      expected_value:
        tag: expected_value
        value: soluble inorganic material name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram, microgram, mole per liter, gram per liter, parts per million
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of substances such as ammonia, road-salt, sea-salt,
      cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.
    title: soluble inorganic material
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soluble inorganic material
    rank: 364
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000672
    alias: soluble_inorg_mat
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  soluble_org_mat:
    name: soluble_org_mat
    annotations:
      expected_value:
        tag: expected_value
        value: soluble organic material name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram, microgram, mole per liter, gram per liter, parts per million
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of substances such as urea, fruit sugars, soluble proteins,
      drugs, pharmaceuticals, etc.
    title: soluble organic material
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - soluble organic material
    rank: 365
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000673
    alias: soluble_org_mat
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    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]+)$
  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: WastewaterSludgeInterface
    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
  suspend_solids:
    name: suspend_solids
    annotations:
      expected_value:
        tag: expected_value
        value: suspended solid name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: gram, microgram, milligram per liter, mole per liter, gram per liter,
          part per million
      occurrence:
        tag: occurrence
        value: m
    description: Concentration of substances including a wide variety of material,
      such as silt, decaying plant and animal matter; can include multiple substances
    title: suspended solids
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - suspended solids
    rank: 372
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000150
    alias: suspend_solids
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - WastewaterSludgeInterface
    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]+)$
  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: WastewaterSludgeInterface
    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.*$
  tertiary_treatment:
    name: tertiary_treatment
    annotations:
      expected_value:
        tag: expected_value
        value: tertiary treatment type
      occurrence:
        tag: occurrence
        value: '1'
    description: The process providing a final treatment stage to raise the effluent
      quality before it is discharged to the receiving environment
    title: tertiary treatment
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - tertiary treatment
    rank: 374
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000352
    alias: tertiary_treatment
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  tot_nitro:
    name: tot_nitro
    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 concentration of water samples, calculated by: total
      nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured
      without filtering, reported as nitrogen'
    title: total nitrogen concentration
    examples:
    - value: 50 micromole per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total nitrogen concentration
    rank: 377
    is_a: core field
    slot_uri: MIXS:0000102
    alias: tot_nitro
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  tot_phosphate:
    name: tot_phosphate
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: microgram per liter, micromole per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Total amount or concentration of phosphate
    title: total phosphate
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - total phosphate
    rank: 378
    is_a: core field
    slot_uri: MIXS:0000689
    alias: tot_phosphate
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  wastewater_type:
    name: wastewater_type
    annotations:
      expected_value:
        tag: expected_value
        value: wastewater type name
      occurrence:
        tag: occurrence
        value: '1'
    description: The origin of wastewater such as human waste, rainfall, storm drains,
      etc.
    title: wastewater type
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - wastewater type
    rank: 385
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000353
    alias: wastewater_type
    owner: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - WastewaterSludgeInterface
    slot_group: mixs_core_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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    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: WastewaterSludgeInterface
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    multivalued: false
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'