Class: Plant Associated (PlantAssociatedInterface)

name: PlantAssociatedInterface
annotations:
  excel_worksheet_name:
    tag: excel_worksheet_name
    value: plant-associated
description: plant_associated dh_interface
title: Plant Associated
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
- SampIdNewTermsMixin
slots:
- air_temp_regm
- ances_data
- antibiotic_regm
- biol_stat
- biotic_regm
- biotic_relationship
- chem_administration
- chem_mutagen
- climate_environment
- collection_date
- collection_date_inc
- collection_time
- cult_root_med
- depth
- ecosystem
- ecosystem_category
- ecosystem_subtype
- ecosystem_type
- elev
- env_broad_scale
- env_local_scale
- env_medium
- experimental_factor
- fertilizer_regm
- fungicide_regm
- gaseous_environment
- genetic_mod
- geo_loc_name
- gravity
- growth_facil
- growth_habit
- growth_hormone_regm
- herbicide_regm
- host_age
- host_common_name
- host_disease_stat
- host_dry_mass
- host_genotype
- host_height
- host_length
- host_life_stage
- host_phenotype
- host_subspecf_genlin
- host_symbiont
- host_taxid
- host_tot_mass
- host_wet_mass
- humidity_regm
- isotope_exposure
- lat_lon
- light_regm
- mechanical_damage
- mineral_nutr_regm
- misc_param
- non_min_nutr_regm
- organism_count
- oxy_stat_samp
- perturbation
- pesticide_regm
- ph_regm
- plant_growth_med
- plant_product
- plant_sex
- plant_struc
- radiation_regm
- rainfall_regm
- root_cond
- root_med_carbon
- root_med_macronutr
- root_med_micronutr
- root_med_ph
- root_med_regl
- root_med_solid
- root_med_suppl
- salinity
- salinity_meth
- salt_regm
- samp_capt_status
- samp_collec_device
- samp_collec_method
- samp_dis_stage
- samp_mat_process
- samp_size
- samp_store_dur
- samp_store_loc
- samp_store_temp
- sample_link
- season_environment
- size_frac
- specific_ecosystem
- standing_water_regm
- start_date_inc
- temp
- tiss_cult_growth_med
- water_temp_regm
- watering_regm
slot_usage:
  air_temp_regm:
    name: air_temp_regm
    annotations:
      expected_value:
        tag: expected_value
        value: temperature value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: meter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to varying temperatures;
      should include the temperature, treatment regimen including how many times the
      treatment was repeated, how long each treatment lasted, and the start and end
      time of the entire treatment; can include different temperature regimens
    title: air temperature regimen
    examples:
    - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - air temperature regimen
    rank: 16
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000551
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  ances_data:
    name: ances_data
    annotations:
      expected_value:
        tag: expected_value
        value: free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about either pedigree or other ancestral information
      description (e.g. parental variety in case of mutant or selection), e.g. A/3*B
      (meaning [(A x B) x B] x B)
    title: ancestral data
    examples:
    - value: A/3*B
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - ancestral data
    rank: 237
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000247
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  antibiotic_regm:
    name: antibiotic_regm
    annotations:
      expected_value:
        tag: expected_value
        value: antibiotic name;antibiotic amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: milligram
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving antibiotic administration;
      should include the name of antibiotic, amount administered, treatment regimen
      including how many times the treatment was repeated, how long each treatment
      lasted, and the start and end time of the entire treatment; can include multiple
      antibiotic regimens
    title: antibiotic regimen
    examples:
    - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - antibiotic regimen
    rank: 238
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000553
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  biol_stat:
    name: biol_stat
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: The level of genome modification.
    title: biological status
    examples:
    - value: natural
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - biological status
    rank: 239
    is_a: core field
    slot_uri: MIXS:0000858
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: biol_stat_enum
    multivalued: false
  biotic_regm:
    name: biotic_regm
    annotations:
      expected_value:
        tag: expected_value
        value: free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about treatment(s) involving use of biotic factors, such
      as bacteria, viruses or fungi.
    title: biotic regimen
    examples:
    - value: sample inoculated with Rhizobium spp. Culture
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - biotic regimen
    rank: 13
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001038
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  biotic_relationship:
    name: biotic_relationship
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
    description: Description of relationship(s) between the subject organism and other
      organism(s) it is associated with. E.g., parasite on species X; mutualist with
      species Y. The target organism is the subject of the relationship, and the other
      organism(s) is the object
    title: observed biotic relationship
    examples:
    - value: free living
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - observed biotic relationship
    rank: 22
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000028
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: biotic_relationship_enum
    multivalued: false
  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_mutagen:
    name: chem_mutagen
    annotations:
      expected_value:
        tag: expected_value
        value: mutagen name;mutagen amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Treatment involving use of mutagens; should include the name of mutagen,
      amount administered, treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment; can include multiple mutagen regimens
    title: chemical mutagen
    examples:
    - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chemical mutagen
    rank: 240
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000555
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  climate_environment:
    name: climate_environment
    annotations:
      expected_value:
        tag: expected_value
        value: climate name;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Treatment involving an exposure to a particular climate; treatment
      regimen including how many times the treatment was repeated, how long each treatment
      lasted, and the start and end time of the entire treatment; can include multiple
      climates
    title: climate environment
    todos:
    - description says "can include multiple climates" but multivalued is set to false
    - add examples, i need to see some examples to add correctly formatted example.
    - description says "can include multiple climates" but multivalued is set to false
    - add examples, i need to see some examples to add correctly formatted example.
    examples:
    - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - climate environment
    rank: 19
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001040
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  collection_date:
    name: collection_date
    annotations:
      expected_value:
        tag: expected_value
        value: date and time
    description: The date of sampling
    title: collection date
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only
    - Use modified term (amended definition)
    examples:
    - value: '2021-04-15'
    - value: 2021-04
    - value: '2021'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - collection date
    rank: 3
    is_a: environment field
    string_serialization: '{date, arbitrary precision}'
    slot_uri: MIXS:0000011
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  collection_date_inc:
    name: collection_date_inc
    description: Date the incubation was harvested/collected/ended. Only relevant
      for incubation samples.
    title: incubation collection date
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
      date only
    comments:
    - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
      are all acceptable.
    examples:
    - value: 2021-04-15, 2021-04 and 2021 are all acceptable.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 2
    string_serialization: '{date, arbitrary precision}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  collection_time:
    name: collection_time
    description: The time of sampling, either as an instance (single point) or interval.
    title: collection time, GMT
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
      time only
    comments:
    - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
    examples:
    - value: 13:33 or 13:33:55
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 1
    string_serialization: '{time, seconds optional}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
  cult_root_med:
    name: cult_root_med
    annotations:
      expected_value:
        tag: expected_value
        value: name, PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Name or reference for the hydroponic or in vitro culture rooting
      medium; can be the name of a commonly used medium or reference to a specific
      medium, e.g. Murashige and Skoog medium. If the medium has not been formally
      published, use the rooting medium descriptors.
    title: culture rooting medium
    examples:
    - value: http://himedialabs.com/TD/PT158.pdf
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - culture rooting medium
    rank: 241
    is_a: core field
    string_serialization: '{text}|{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0001041
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  depth:
    name: depth
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: The vertical distance below local surface, e.g. for sediment or soil
      samples depth is measured from sediment or soil surface, respectively. Depth
      can be reported as an interval for subsurface samples.
    title: depth, meters
    notes:
    - Use modified term
    comments:
    - All depths must be reported in meters. Provide the numerical portion only.
    examples:
    - value: 0 - 0.1
    - value: '1'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - depth
    rank: 9
    is_a: environment field
    string_serialization: '{float}|{float}-{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
  elev:
    name: elev
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit.
    title: elevation, meters
    comments:
    - All elevations must be reported in meters. Provide the numerical portion only.
    - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,
      if needed, to help estimate the elevation based on latitude and longitude coordinates.
    examples:
    - value: '225'
    - value: '0'
    - value: '1250'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - elevation
    rank: 6
    is_a: environment field
    slot_uri: MIXS:0000093
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: float
    required: true
    multivalued: false
  env_broad_scale:
    name: env_broad_scale
    annotations:
      expected_value:
        tag: expected_value
        value: The major environment type(s) where the sample was collected. Recommend
          subclasses of biome [ENVO:00000428]. Multiple terms can be separated by
          one or more pipes.
      tooltip:
        tag: tooltip
        value: The biome or major environmental system where the sample or specimen
          originated. Choose values from subclasses of the 'biome' class [ENVO:00000428]
          in the Environment Ontology (ENVO). For host-associated or plant-associated
          samples, use terms from the UBERON or Plant Ontology to describe the broad
          anatomical or morphological context
    description: 'In this field, report which major environmental system your sample
      or specimen came from. The systems identified should have a coarse spatial grain,
      to provide the general environmental context of where the sampling was done
      (e.g. were you in the desert or a rainforest?). We recommend using subclasses
      of ENVO''s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format
      (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel
      [termID]|termLabel [termID]. Example: Annotating a water sample from the photic
      zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome
      [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider:
      tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new
      terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html'
    title: broad-scale environmental context
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water
        sample from the photic zone in middle of the Atlantic Ocean
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - broad-scale environmental context
    rank: 6
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  env_local_scale:
    name: env_local_scale
    annotations:
      expected_value:
        tag: expected_value
        value: Environmental entities having causal influences upon the entity at
          time of sampling.
      tooltip:
        tag: tooltip
        value: The specific environmental entities or features near the sample or
          specimen that significantly influence its characteristics or composition.
          These entities are typically smaller in scale than the broad environmental
          context. Values for this field should be countable, material nouns and must
          be chosen from subclasses of BFO:0000040 (material entity) that appear in
          the Environment Ontology (ENVO). For host-associated or plant-associated
          samples, use terms from the UBERON or Plant Ontology to describe specific
          anatomical structures or plant parts.
    description: 'Report the entity or entities which are in the sample or specimen’s
      local vicinity and which you believe have significant causal influences on your
      sample or specimen. We recommend using EnvO terms which are of smaller spatial
      grain than your entry for env_broad_scale. Terms, such as anatomical sites,
      from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON)
      are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'
    title: local environmental context
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: canopy [ENVO:00000047]
    - value: herb and fern layer [ENVO:01000337]
    - value: litter layer [ENVO:01000338]
    - value: understory [01000335]
    - value: shrub layer [ENVO:01000336]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - local environmental context
    rank: 7
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000013
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  env_medium:
    name: env_medium
    annotations:
      expected_value:
        tag: expected_value
        value: The material displaced by the entity at time of sampling. Recommend
          subclasses of environmental material [ENVO:00010483].
      tooltip:
        tag: tooltip
        value: The predominant environmental material or substrate that directly surrounds
          or hosts the sample or specimen at the time of sampling. Choose values from
          subclasses of the 'environmental material' class [ENVO:00010483] in the
          Environment Ontology (ENVO). Values for this field should be measurable
          or mass material nouns, representing continuous environmental materials.
          For host-associated or plant-associated samples, use terms from the UBERON
          or Plant Ontology to indicate a tissue, organ, or plant structure
    description: 'Report the environmental material(s) immediately surrounding the
      sample or specimen at the time of sampling. We recommend using subclasses of
      ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
      documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
      . Terms from other OBO ontologies are permissible as long as they reference
      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
      (e.g. a tree, a leaf, a table top).'
    title: environmental medium
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: soil [ENVO:00001998]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - environmental medium
    rank: 8
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000014
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  experimental_factor:
    name: experimental_factor
    annotations:
      expected_value:
        tag: expected_value
        value: text or EFO and/or OBI
    description: Experimental factors are essentially the variable aspects of an experiment
      design which can be used to describe an experiment, or set of experiments, in
      an increasingly detailed manner. This field accepts ontology terms from Experimental
      Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For
      a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;
      for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
    title: experimental factor
    examples:
    - value: time series design [EFO:EFO_0001779]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - experimental factor
    rank: 12
    is_a: investigation field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000008
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  fertilizer_regm:
    name: fertilizer_regm
    annotations:
      expected_value:
        tag: expected_value
        value: fertilizer name;fertilizer amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving the use of fertilizers; should
      include the name of fertilizer, amount administered, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple fertilizer
      regimens
    title: fertilizer regimen
    examples:
    - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - fertilizer regimen
    rank: 242
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000556
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  fungicide_regm:
    name: fungicide_regm
    annotations:
      expected_value:
        tag: expected_value
        value: fungicide name;fungicide amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of fungicides; should include
      the name of fungicide, amount administered, treatment regimen including how
      many times the treatment was repeated, how long each treatment lasted, and the
      start and end time of the entire treatment; can include multiple fungicide regimens
    title: fungicide regimen
    examples:
    - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - fungicide regimen
    rank: 243
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000557
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  gaseous_environment:
    name: gaseous_environment
    annotations:
      expected_value:
        tag: expected_value
        value: gaseous compound name;gaseous compound amount;treatment interval and
          duration
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: m
    description: Use of conditions with differing gaseous environments; should include
      the name of gaseous compound, amount administered, treatment duration, interval
      and total experimental duration; can include multiple gaseous environment regimens
    title: gaseous environment
    todos:
    - would like to see usage examples for this slot. Requiring micromole/L seems
      too limiting and doesn't match expected_value value
    - did I do this right? keep the example that's provided and add another? so as
      to not override
    - would like to see usage examples for this slot. Requiring micromole/L seems
      too limiting and doesn't match expected_value value
    - did I do this right? keep the example that's provided and add another? so as
      to not override
    examples:
    - value: CO2; 500ppm above ambient; constant
    - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gaseous environment
    rank: 20
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000558
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  genetic_mod:
    name: genetic_mod
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url or free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Genetic modifications of the genome of an organism, which may occur
      naturally by spontaneous mutation, or be introduced by some experimental means,
      e.g. specification of a transgene or the gene knocked-out or details of transient
      transfection
    title: genetic modification
    examples:
    - value: aox1A transgenic
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - genetic modification
    rank: 244
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0000859
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  geo_loc_name:
    name: geo_loc_name
    annotations:
      expected_value:
        tag: expected_value
        value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location
          name'
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name.
    title: geographic location (country and/or sea,region)
    examples:
    - value: 'USA: Maryland, Bethesda'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - geographic location (country and/or sea,region)
    rank: 4
    is_a: environment field
    string_serialization: '{text}: {text}, {text}'
    slot_uri: MIXS:0000010
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  gravity:
    name: gravity
    annotations:
      expected_value:
        tag: expected_value
        value: gravity factor value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: meter per square second, g
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of gravity factor to study
      various types of responses in presence, absence or modified levels of gravity;
      treatment regimen including how many times the treatment was repeated, how long
      each treatment lasted, and the start and end time of the entire treatment; can
      include multiple treatments
    title: gravity
    examples:
    - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gravity
    rank: 245
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000559
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  growth_facil:
    name: growth_facil
    annotations:
      expected_value:
        tag: expected_value
        value: free text or CO
      occurrence:
        tag: occurrence
        value: '1'
    description: 'Type of facility/location where the sample was harvested; controlled
      vocabulary: growth chamber, open top chamber, glasshouse, experimental garden,
      field.'
    title: growth facility
    notes:
    - 'Removed from description: Alternatively use Crop Ontology (CO) terms'
    examples:
    - value: Growth chamber [CO_715:0000189]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - growth facility
    rank: 1
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001043
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: GrowthFacilEnum
    required: true
    multivalued: false
  growth_habit:
    name: growth_habit
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Characteristic shape, appearance or growth form of a plant species
    title: growth habit
    examples:
    - value: spreading
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - growth habit
    rank: 246
    is_a: core field
    slot_uri: MIXS:0001044
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: growth_habit_enum
    multivalued: false
  growth_hormone_regm:
    name: growth_hormone_regm
    annotations:
      expected_value:
        tag: expected_value
        value: growth hormone name;growth hormone amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of growth hormones; should
      include the name of growth hormone, amount administered, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple growth
      hormone regimens
    title: growth hormone regimen
    examples:
    - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - growth hormone regimen
    rank: 247
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000560
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  herbicide_regm:
    name: herbicide_regm
    annotations:
      expected_value:
        tag: expected_value
        value: herbicide name;herbicide amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of herbicides; information
      about treatment involving use of growth hormones; should include the name of
      herbicide, amount administered, treatment regimen including how many times the
      treatment was repeated, how long each treatment lasted, and the start and end
      time of the entire treatment; can include multiple regimens
    title: herbicide regimen
    examples:
    - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - herbicide regimen
    rank: 248
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000561
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_age:
    name: host_age
    annotations:
      expected_value:
        tag: expected_value
        value: value
      preferred_unit:
        tag: preferred_unit
        value: year, day, hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Age of host at the time of sampling; relevant scale depends on species
      and study, e.g. Could be seconds for amoebae or centuries for trees
    title: host age
    examples:
    - value: 10 days
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host age
    rank: 249
    is_a: core field
    slot_uri: MIXS:0000255
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_common_name:
    name: host_common_name
    annotations:
      expected_value:
        tag: expected_value
        value: common name
      occurrence:
        tag: occurrence
        value: '1'
    description: Common name of the host.
    title: host common name
    examples:
    - value: human
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host common name
    rank: 250
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000248
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_disease_stat:
    name: host_disease_stat
    annotations:
      expected_value:
        tag: expected_value
        value: disease name or Disease Ontology term
    description: List of diseases with which the host has been diagnosed; can include
      multiple diagnoses. The value of the field depends on host; for humans the terms
      should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
      non-human host diseases are free text
    title: host disease status
    examples:
    - value: rabies [DOID:11260]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host disease status
    rank: 390
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000031
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_dry_mass:
    name: host_dry_mass
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: kilogram, gram
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of dry mass
    title: host dry mass
    examples:
    - value: 500 gram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host dry mass
    rank: 251
    is_a: core field
    slot_uri: MIXS:0000257
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_genotype:
    name: host_genotype
    annotations:
      expected_value:
        tag: expected_value
        value: genotype
      occurrence:
        tag: occurrence
        value: '1'
    description: Observed genotype
    title: host genotype
    examples:
    - value: C57BL/6
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host genotype
    rank: 252
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000365
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_height:
    name: host_height
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: centimeter, millimeter, meter
      occurrence:
        tag: occurrence
        value: '1'
    description: The height of subject
    title: host height
    examples:
    - value: 0.1 meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host height
    rank: 253
    is_a: core field
    slot_uri: MIXS:0000264
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_length:
    name: host_length
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: centimeter, millimeter, meter
      occurrence:
        tag: occurrence
        value: '1'
    description: The length of subject
    title: host length
    examples:
    - value: 1 meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host length
    rank: 254
    is_a: core field
    slot_uri: MIXS:0000256
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_life_stage:
    name: host_life_stage
    annotations:
      expected_value:
        tag: expected_value
        value: stage
      occurrence:
        tag: occurrence
        value: '1'
    description: Description of life stage of host
    title: host life stage
    examples:
    - value: adult
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host life stage
    rank: 255
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000251
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_phenotype:
    name: host_phenotype
    annotations:
      expected_value:
        tag: expected_value
        value: PATO or HP
      occurrence:
        tag: occurrence
        value: '1'
    description: Phenotype of human or other host. For phenotypic quality ontology
      (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato.
      For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP
    title: host phenotype
    examples:
    - value: elongated [PATO:0001154]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host phenotype
    rank: 256
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000874
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  host_subspecf_genlin:
    name: host_subspecf_genlin
    annotations:
      expected_value:
        tag: expected_value
        value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,
          e.g. serovar, biotype, ecotype, variety, cultivar.
      occurrence:
        tag: occurrence
        value: m
    description: Information about the genetic distinctness of the host organism below
      the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,
      or any relevant genetic typing schemes like Group I plasmid. Subspecies should
      not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage
      name and the lineage rank separated by a colon, e.g., biovar:abc123.
    title: host subspecific genetic lineage
    examples:
    - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host subspecific genetic lineage
    rank: 257
    is_a: core field
    string_serialization: '{rank name}:{text}'
    slot_uri: MIXS:0001318
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_symbiont:
    name: host_symbiont
    annotations:
      expected_value:
        tag: expected_value
        value: species name or common name
      occurrence:
        tag: occurrence
        value: m
    description: The taxonomic name of the organism(s) found living in mutualistic,
      commensalistic, or parasitic symbiosis with the specific host.
    title: observed host symbionts
    examples:
    - value: flukeworms
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - observed host symbionts
    rank: 258
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001298
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_taxid:
    name: host_taxid
    annotations:
      expected_value:
        tag: expected_value
        value: NCBI taxon identifier
      occurrence:
        tag: occurrence
        value: '1'
    description: NCBI taxon id of the host, e.g. 9606
    title: host taxid
    comments:
    - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host taxid
    rank: 259
    is_a: core field
    slot_uri: MIXS:0000250
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_tot_mass:
    name: host_tot_mass
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: kilogram, gram
      occurrence:
        tag: occurrence
        value: '1'
    description: Total mass of the host at collection, the unit depends on host
    title: host total mass
    examples:
    - value: 2500 gram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host total mass
    rank: 260
    is_a: core field
    slot_uri: MIXS:0000263
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_wet_mass:
    name: host_wet_mass
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: kilogram, gram
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of wet mass
    title: host wet mass
    examples:
    - value: 1500 gram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host wet mass
    rank: 261
    is_a: core field
    slot_uri: MIXS:0000567
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  humidity_regm:
    name: humidity_regm
    annotations:
      expected_value:
        tag: expected_value
        value: humidity value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram per cubic meter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to varying degree
      of humidity; information about treatment involving use of growth hormones; should
      include amount of humidity administered, treatment regimen including how many
      times the treatment was repeated, how long each treatment lasted, and the start
      and end time of the entire treatment; can include multiple regimens
    title: humidity regimen
    examples:
    - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - humidity regimen
    rank: 21
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000568
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  isotope_exposure:
    name: isotope_exposure
    description: List isotope exposure or addition applied to your sample.
    title: isotope exposure/addition
    todos:
    - Can we make the H218O correctly super and subscripted?
    comments:
    - This is required when your experimental design includes the use of isotopically
      labeled compounds
    examples:
    - value: 13C glucose
    - value: H218O
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000751
    rank: 16
    string_serialization: '{termLabel} {[termID]}; {timestamp}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
  lat_lon:
    name: lat_lon
    annotations:
      expected_value:
        tag: expected_value
        value: decimal degrees,  limit to 8 decimal points
    description: The geographical origin of the sample as defined by latitude and
      longitude. The values should be reported in decimal degrees and in WGS84 system
    title: geographic location (latitude and longitude)
    notes:
    - This is currently a required field but it's not clear if this should be required
      for human hosts
    examples:
    - value: 50.586825 6.408977
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - geographic location (latitude and longitude)
    rank: 5
    is_a: environment field
    string_serialization: '{lat lon}'
    slot_uri: MIXS:0000009
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$
  light_regm:
    name: light_regm
    annotations:
      expected_value:
        tag: expected_value
        value: exposure type;light intensity;light quality
      preferred_unit:
        tag: preferred_unit
        value: lux; micrometer, nanometer, angstrom
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about treatment(s) involving exposure to light, including
      both light intensity and quality.
    title: light regimen
    examples:
    - value: incandescant light;10 lux;450 nanometer
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - light regimen
    rank: 24
    is_a: core field
    string_serialization: '{text};{float} {unit};{float} {unit}'
    slot_uri: MIXS:0000569
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      \S+$
  mechanical_damage:
    name: mechanical_damage
    annotations:
      expected_value:
        tag: expected_value
        value: damage type;body site
      occurrence:
        tag: occurrence
        value: m
    description: Information about any mechanical damage exerted on the plant; can
      include multiple damages and sites
    title: mechanical damage
    examples:
    - value: pruning;bark
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mechanical damage
    rank: 262
    is_a: core field
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0001052
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  mineral_nutr_regm:
    name: mineral_nutr_regm
    annotations:
      expected_value:
        tag: expected_value
        value: mineral nutrient name;mineral nutrient amount;treatment interval and
          duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving the use of mineral supplements;
      should include the name of mineral nutrient, amount administered, treatment
      regimen including how many times the treatment was repeated, how long each treatment
      lasted, and the start and end time of the entire treatment; can include multiple
      mineral nutrient regimens
    title: mineral nutrient regimen
    examples:
    - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mineral nutrient regimen
    rank: 263
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000570
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  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]+)$
  non_min_nutr_regm:
    name: non_min_nutr_regm
    annotations:
      expected_value:
        tag: expected_value
        value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval
          and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving the exposure of plant to non-mineral
      nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral
      nutrient, amount administered, treatment regimen including how many times the
      treatment was repeated, how long each treatment lasted, and the start and end
      time of the entire treatment; can include multiple non-mineral nutrient regimens
    title: non-mineral nutrient regimen
    examples:
    - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - non-mineral nutrient regimen
    rank: 264
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000571
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  organism_count:
    name: organism_count
    annotations:
      expected_value:
        tag: expected_value
        value: organism name;measurement value;enumeration
      preferred_unit:
        tag: preferred_unit
        value: number of cells per cubic meter, number of cells per milliliter, number
          of cells per cubic centimeter
      occurrence:
        tag: occurrence
        value: m
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organism count
    rank: 30
    is_a: core field
    slot_uri: MIXS:0000103
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$
  oxy_stat_samp:
    name: oxy_stat_samp
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Oxygenation status of sample
    title: oxygenation status of sample
    examples:
    - value: aerobic
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - oxygenation status of sample
    rank: 25
    is_a: core field
    slot_uri: MIXS:0000753
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: OxyStatSampEnum
    multivalued: false
  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
  pesticide_regm:
    name: pesticide_regm
    annotations:
      expected_value:
        tag: expected_value
        value: pesticide name;pesticide amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of insecticides; should
      include the name of pesticide, amount administered, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple pesticide
      regimens
    title: pesticide regimen
    examples:
    - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pesticide regimen
    rank: 265
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000573
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  ph_regm:
    name: ph_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving exposure of plants to varying
      levels of ph of the growth media, treatment regimen including how many times
      the treatment was repeated, how long each treatment lasted, and the start and
      end time of the entire treatment; can include multiple regimen
    title: pH regimen
    examples:
    - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pH regimen
    rank: 266
    is_a: core field
    string_serialization: '{float};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001056
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  plant_growth_med:
    name: plant_growth_med
    annotations:
      expected_value:
        tag: expected_value
        value: EO or enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Specification of the media for growing the plants or tissue cultured
      samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in
      vitro liquid culture medium. Recommended value is a specific value from EO:plant
      growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147)
      or other controlled vocabulary
    title: plant growth medium
    examples:
    - value: hydroponic plant culture media [EO:0007067]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - plant growth medium
    rank: 267
    is_a: core field
    slot_uri: MIXS:0001057
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  plant_product:
    name: plant_product
    annotations:
      expected_value:
        tag: expected_value
        value: product name
      occurrence:
        tag: occurrence
        value: '1'
    description: Substance produced by the plant, where the sample was obtained from
    title: plant product
    examples:
    - value: xylem sap [PO:0025539]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - plant product
    rank: 268
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001058
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  plant_sex:
    name: plant_sex
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Sex of the reproductive parts on the whole plant, e.g. pistillate,
      staminate, monoecieous, hermaphrodite.
    title: plant sex
    examples:
    - value: Hermaphroditic
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - plant sex
    rank: 269
    is_a: core field
    slot_uri: MIXS:0001059
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: plant_sex_enum
    multivalued: false
  plant_struc:
    name: plant_struc
    annotations:
      expected_value:
        tag: expected_value
        value: PO
      occurrence:
        tag: occurrence
        value: '1'
    description: Name of plant structure the sample was obtained from; for Plant Ontology
      (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,
      e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the
      sex of it can be recorded here.
    title: plant structure
    examples:
    - value: epidermis [PO:0005679]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - plant structure
    rank: 270
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001060
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  radiation_regm:
    name: radiation_regm
    annotations:
      expected_value:
        tag: expected_value
        value: radiation type name;radiation amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: rad, gray
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving exposure of plant or a plant
      part to a particular radiation regimen; should include the radiation type, amount
      or intensity administered, treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment; can include multiple radiation regimens
    title: radiation regimen
    examples:
    - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - radiation regimen
    rank: 271
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000575
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  rainfall_regm:
    name: rainfall_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: millimeter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to a given amount
      of rainfall, treatment regimen including how many times the treatment was repeated,
      how long each treatment lasted, and the start and end time of the entire treatment;
      can include multiple regimens
    title: rainfall regimen
    examples:
    - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rainfall regimen
    rank: 272
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000576
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  root_cond:
    name: root_cond
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url or free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Relevant rooting conditions such as field plot size, sowing density,
      container dimensions, number of plants per container.
    title: rooting conditions
    examples:
    - value: http://himedialabs.com/TD/PT158.pdf
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting conditions
    rank: 273
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001061
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  root_med_carbon:
    name: root_med_carbon
    annotations:
      expected_value:
        tag: expected_value
        value: carbon source name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Source of organic carbon in the culture rooting medium; e.g. sucrose.
    title: rooting medium carbon
    examples:
    - value: sucrose
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium carbon
    rank: 274
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000577
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  root_med_macronutr:
    name: root_med_macronutr
    annotations:
      expected_value:
        tag: expected_value
        value: macronutrient name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of the culture rooting medium macronutrients (N,P, K,
      Ca, Mg, S); e.g. KH2PO4 (170 mg/L).
    title: rooting medium macronutrients
    examples:
    - value: KH2PO4;170 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium macronutrients
    rank: 275
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000578
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  root_med_micronutr:
    name: root_med_micronutr
    annotations:
      expected_value:
        tag: expected_value
        value: micronutrient name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of the culture rooting medium micronutrients (Fe, Mn,
      Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L).
    title: rooting medium micronutrients
    examples:
    - value: H3BO3;6.2 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium micronutrients
    rank: 276
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000579
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  root_med_ph:
    name: root_med_ph
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    description: pH measurement of the culture rooting medium; e.g. 5.5.
    title: rooting medium pH
    examples:
    - value: '7.5'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium pH
    rank: 277
    is_a: core field
    slot_uri: MIXS:0001062
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  root_med_regl:
    name: root_med_regl
    annotations:
      expected_value:
        tag: expected_value
        value: regulator name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Growth regulators in the culture rooting medium such as cytokinins,
      auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA.
    title: rooting medium regulators
    examples:
    - value: abscisic acid;0.75 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium regulators
    rank: 278
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000581
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  root_med_solid:
    name: root_med_solid
    annotations:
      expected_value:
        tag: expected_value
        value: name
      occurrence:
        tag: occurrence
        value: '1'
    description: Specification of the solidifying agent in the culture rooting medium;
      e.g. agar.
    title: rooting medium solidifier
    examples:
    - value: agar
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium solidifier
    rank: 279
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001063
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  root_med_suppl:
    name: root_med_suppl
    annotations:
      expected_value:
        tag: expected_value
        value: supplement name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Organic supplements of the culture rooting medium, such as vitamins,
      amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid
      (0.5 mg/L).
    title: rooting medium organic supplements
    examples:
    - value: nicotinic acid;0.5 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium organic supplements
    rank: 280
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000580
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  salinity:
    name: salinity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: practical salinity unit, percentage
      occurrence:
        tag: occurrence
        value: '1'
    description: The total concentration of all dissolved salts in a liquid or solid
      sample. While salinity can be measured by a complete chemical analysis, this
      method is difficult and time consuming. More often, it is instead derived from
      the conductivity measurement. This is known as practical salinity. These derivations
      compare the specific conductance of the sample to a salinity standard such as
      seawater.
    title: salinity
    examples:
    - value: 25 practical salinity unit
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - salinity
    rank: 54
    is_a: core field
    slot_uri: MIXS:0000183
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  salinity_meth:
    name: salinity_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining salinity
    title: salinity method
    examples:
    - value: https://doi.org/10.1007/978-1-61779-986-0_28
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - salinity method
    rank: 55
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000341
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  salt_regm:
    name: salt_regm
    annotations:
      expected_value:
        tag: expected_value
        value: salt name;salt amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, microgram, mole per liter, gram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of salts as supplement
      to liquid and soil growth media; should include the name of salt, amount administered,
      treatment regimen including how many times the treatment was repeated, how long
      each treatment lasted, and the start and end time of the entire treatment; can
      include multiple salt regimens
    title: salt regimen
    examples:
    - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - salt regimen
    rank: 281
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000582
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  samp_capt_status:
    name: samp_capt_status
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Reason for the sample
    title: sample capture status
    examples:
    - value: farm sample
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample capture status
    rank: 282
    is_a: core field
    slot_uri: MIXS:0000860
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: samp_capt_status_enum
    multivalued: false
  samp_collec_device:
    name: samp_collec_device
    annotations:
      expected_value:
        tag: expected_value
        value: device name
    description: The device used to collect an environmental sample. This field accepts
      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
    title: sample collection device
    comments:
    - Report dimensions and details when applicable
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample collection device
    rank: 14
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000002
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  samp_collec_method:
    name: samp_collec_method
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url , or text
    description: The method employed for collecting the sample.
    title: sample collection method
    comments:
    - This can be a citation or description
    examples:
    - value: swabbing
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample collection method
    rank: 15
    is_a: nucleic acid sequence source field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001225
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
  samp_dis_stage:
    name: samp_dis_stage
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Stage of the disease at the time of sample collection, e.g. inoculation,
      penetration, infection, growth and reproduction, dissemination of pathogen.
    title: sample disease stage
    examples:
    - value: infection
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample disease stage
    rank: 283
    is_a: core field
    slot_uri: MIXS:0000249
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: samp_dis_stage_enum
    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]+'
  season_environment:
    name: season_environment
    annotations:
      expected_value:
        tag: expected_value
        value: seasonal environment name;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Treatment involving an exposure to a particular season (e.g. Winter,
      summer, rabi, rainy etc.), treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment
    title: seasonal environment
    examples:
    - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - seasonal environment
    rank: 284
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001068
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    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
  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
  standing_water_regm:
    name: standing_water_regm
    annotations:
      expected_value:
        tag: expected_value
        value: standing water type;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Treatment involving an exposure to standing water during a plant's
      life span, types can be flood water or standing water, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple regimens
    title: standing water regimen
    examples:
    - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - standing water regimen
    rank: 286
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001069
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  start_date_inc:
    name: start_date_inc
    description: Date the incubation was started. Only relevant for incubation samples.
    title: incubation start date
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
      date only
    comments:
    - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
      are all acceptable.
    examples:
    - value: 2021-04-15, 2021-04 and 2021 are all acceptable.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 4
    string_serialization: '{date, arbitrary precision}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  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.*$
  tiss_cult_growth_med:
    name: tiss_cult_growth_med
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url or free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Description of plant tissue culture growth media used
    title: tissue culture growth media
    examples:
    - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - tissue culture growth media
    rank: 287
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001070
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  water_temp_regm:
    name: water_temp_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to water with varying
      degree of temperature, treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment; can include multiple regimens
    title: water temperature regimen
    examples:
    - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - water temperature regimen
    rank: 288
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000590
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  watering_regm:
    name: watering_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: milliliter, liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to watering frequencies,
      treatment regimen including how many times the treatment was repeated, how long
      each treatment lasted, and the start and end time of the entire treatment; can
      include multiple regimens
    title: watering regimen
    examples:
    - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    - value: 75% water holding capacity; constant
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - watering regimen
    rank: 25
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000591
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  horizon_meth:
    name: horizon_meth
    title: horizon method

name: PlantAssociatedInterface
annotations:
  excel_worksheet_name:
    tag: excel_worksheet_name
    value: plant-associated
description: plant_associated dh_interface
title: Plant Associated
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
- SampIdNewTermsMixin
slot_usage:
  air_temp_regm:
    name: air_temp_regm
    annotations:
      expected_value:
        tag: expected_value
        value: temperature value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: meter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to varying temperatures;
      should include the temperature, treatment regimen including how many times the
      treatment was repeated, how long each treatment lasted, and the start and end
      time of the entire treatment; can include different temperature regimens
    title: air temperature regimen
    examples:
    - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - air temperature regimen
    rank: 16
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000551
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  ances_data:
    name: ances_data
    annotations:
      expected_value:
        tag: expected_value
        value: free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about either pedigree or other ancestral information
      description (e.g. parental variety in case of mutant or selection), e.g. A/3*B
      (meaning [(A x B) x B] x B)
    title: ancestral data
    examples:
    - value: A/3*B
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - ancestral data
    rank: 237
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000247
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  antibiotic_regm:
    name: antibiotic_regm
    annotations:
      expected_value:
        tag: expected_value
        value: antibiotic name;antibiotic amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: milligram
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving antibiotic administration;
      should include the name of antibiotic, amount administered, treatment regimen
      including how many times the treatment was repeated, how long each treatment
      lasted, and the start and end time of the entire treatment; can include multiple
      antibiotic regimens
    title: antibiotic regimen
    examples:
    - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - antibiotic regimen
    rank: 238
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000553
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  biol_stat:
    name: biol_stat
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: The level of genome modification.
    title: biological status
    examples:
    - value: natural
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - biological status
    rank: 239
    is_a: core field
    slot_uri: MIXS:0000858
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: biol_stat_enum
    multivalued: false
  biotic_regm:
    name: biotic_regm
    annotations:
      expected_value:
        tag: expected_value
        value: free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about treatment(s) involving use of biotic factors, such
      as bacteria, viruses or fungi.
    title: biotic regimen
    examples:
    - value: sample inoculated with Rhizobium spp. Culture
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - biotic regimen
    rank: 13
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001038
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  biotic_relationship:
    name: biotic_relationship
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
    description: Description of relationship(s) between the subject organism and other
      organism(s) it is associated with. E.g., parasite on species X; mutualist with
      species Y. The target organism is the subject of the relationship, and the other
      organism(s) is the object
    title: observed biotic relationship
    examples:
    - value: free living
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - observed biotic relationship
    rank: 22
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000028
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: biotic_relationship_enum
    multivalued: false
  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_mutagen:
    name: chem_mutagen
    annotations:
      expected_value:
        tag: expected_value
        value: mutagen name;mutagen amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Treatment involving use of mutagens; should include the name of mutagen,
      amount administered, treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment; can include multiple mutagen regimens
    title: chemical mutagen
    examples:
    - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chemical mutagen
    rank: 240
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000555
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  climate_environment:
    name: climate_environment
    annotations:
      expected_value:
        tag: expected_value
        value: climate name;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Treatment involving an exposure to a particular climate; treatment
      regimen including how many times the treatment was repeated, how long each treatment
      lasted, and the start and end time of the entire treatment; can include multiple
      climates
    title: climate environment
    todos:
    - description says "can include multiple climates" but multivalued is set to false
    - add examples, i need to see some examples to add correctly formatted example.
    - description says "can include multiple climates" but multivalued is set to false
    - add examples, i need to see some examples to add correctly formatted example.
    examples:
    - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - climate environment
    rank: 19
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001040
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  collection_date:
    name: collection_date
    annotations:
      expected_value:
        tag: expected_value
        value: date and time
    description: The date of sampling
    title: collection date
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only
    - Use modified term (amended definition)
    examples:
    - value: '2021-04-15'
    - value: 2021-04
    - value: '2021'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - collection date
    rank: 3
    is_a: environment field
    string_serialization: '{date, arbitrary precision}'
    slot_uri: MIXS:0000011
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  collection_date_inc:
    name: collection_date_inc
    description: Date the incubation was harvested/collected/ended. Only relevant
      for incubation samples.
    title: incubation collection date
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
      date only
    comments:
    - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
      are all acceptable.
    examples:
    - value: 2021-04-15, 2021-04 and 2021 are all acceptable.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 2
    string_serialization: '{date, arbitrary precision}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  collection_time:
    name: collection_time
    description: The time of sampling, either as an instance (single point) or interval.
    title: collection time, GMT
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
      time only
    comments:
    - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
    examples:
    - value: 13:33 or 13:33:55
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 1
    string_serialization: '{time, seconds optional}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
  cult_root_med:
    name: cult_root_med
    annotations:
      expected_value:
        tag: expected_value
        value: name, PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Name or reference for the hydroponic or in vitro culture rooting
      medium; can be the name of a commonly used medium or reference to a specific
      medium, e.g. Murashige and Skoog medium. If the medium has not been formally
      published, use the rooting medium descriptors.
    title: culture rooting medium
    examples:
    - value: http://himedialabs.com/TD/PT158.pdf
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - culture rooting medium
    rank: 241
    is_a: core field
    string_serialization: '{text}|{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0001041
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  depth:
    name: depth
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: The vertical distance below local surface, e.g. for sediment or soil
      samples depth is measured from sediment or soil surface, respectively. Depth
      can be reported as an interval for subsurface samples.
    title: depth, meters
    notes:
    - Use modified term
    comments:
    - All depths must be reported in meters. Provide the numerical portion only.
    examples:
    - value: 0 - 0.1
    - value: '1'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - depth
    rank: 9
    is_a: environment field
    string_serialization: '{float}|{float}-{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
  elev:
    name: elev
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit.
    title: elevation, meters
    comments:
    - All elevations must be reported in meters. Provide the numerical portion only.
    - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,
      if needed, to help estimate the elevation based on latitude and longitude coordinates.
    examples:
    - value: '225'
    - value: '0'
    - value: '1250'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - elevation
    rank: 6
    is_a: environment field
    slot_uri: MIXS:0000093
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: float
    required: true
    multivalued: false
  env_broad_scale:
    name: env_broad_scale
    annotations:
      expected_value:
        tag: expected_value
        value: The major environment type(s) where the sample was collected. Recommend
          subclasses of biome [ENVO:00000428]. Multiple terms can be separated by
          one or more pipes.
      tooltip:
        tag: tooltip
        value: The biome or major environmental system where the sample or specimen
          originated. Choose values from subclasses of the 'biome' class [ENVO:00000428]
          in the Environment Ontology (ENVO). For host-associated or plant-associated
          samples, use terms from the UBERON or Plant Ontology to describe the broad
          anatomical or morphological context
    description: 'In this field, report which major environmental system your sample
      or specimen came from. The systems identified should have a coarse spatial grain,
      to provide the general environmental context of where the sampling was done
      (e.g. were you in the desert or a rainforest?). We recommend using subclasses
      of ENVO''s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format
      (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel
      [termID]|termLabel [termID]. Example: Annotating a water sample from the photic
      zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome
      [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider:
      tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new
      terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html'
    title: broad-scale environmental context
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water
        sample from the photic zone in middle of the Atlantic Ocean
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - broad-scale environmental context
    rank: 6
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  env_local_scale:
    name: env_local_scale
    annotations:
      expected_value:
        tag: expected_value
        value: Environmental entities having causal influences upon the entity at
          time of sampling.
      tooltip:
        tag: tooltip
        value: The specific environmental entities or features near the sample or
          specimen that significantly influence its characteristics or composition.
          These entities are typically smaller in scale than the broad environmental
          context. Values for this field should be countable, material nouns and must
          be chosen from subclasses of BFO:0000040 (material entity) that appear in
          the Environment Ontology (ENVO). For host-associated or plant-associated
          samples, use terms from the UBERON or Plant Ontology to describe specific
          anatomical structures or plant parts.
    description: 'Report the entity or entities which are in the sample or specimen’s
      local vicinity and which you believe have significant causal influences on your
      sample or specimen. We recommend using EnvO terms which are of smaller spatial
      grain than your entry for env_broad_scale. Terms, such as anatomical sites,
      from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON)
      are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'
    title: local environmental context
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: canopy [ENVO:00000047]
    - value: herb and fern layer [ENVO:01000337]
    - value: litter layer [ENVO:01000338]
    - value: understory [01000335]
    - value: shrub layer [ENVO:01000336]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - local environmental context
    rank: 7
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000013
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  env_medium:
    name: env_medium
    annotations:
      expected_value:
        tag: expected_value
        value: The material displaced by the entity at time of sampling. Recommend
          subclasses of environmental material [ENVO:00010483].
      tooltip:
        tag: tooltip
        value: The predominant environmental material or substrate that directly surrounds
          or hosts the sample or specimen at the time of sampling. Choose values from
          subclasses of the 'environmental material' class [ENVO:00010483] in the
          Environment Ontology (ENVO). Values for this field should be measurable
          or mass material nouns, representing continuous environmental materials.
          For host-associated or plant-associated samples, use terms from the UBERON
          or Plant Ontology to indicate a tissue, organ, or plant structure
    description: 'Report the environmental material(s) immediately surrounding the
      sample or specimen at the time of sampling. We recommend using subclasses of
      ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
      documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
      . Terms from other OBO ontologies are permissible as long as they reference
      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
      (e.g. a tree, a leaf, a table top).'
    title: environmental medium
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: soil [ENVO:00001998]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - environmental medium
    rank: 8
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000014
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: string
    required: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  experimental_factor:
    name: experimental_factor
    annotations:
      expected_value:
        tag: expected_value
        value: text or EFO and/or OBI
    description: Experimental factors are essentially the variable aspects of an experiment
      design which can be used to describe an experiment, or set of experiments, in
      an increasingly detailed manner. This field accepts ontology terms from Experimental
      Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For
      a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;
      for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
    title: experimental factor
    examples:
    - value: time series design [EFO:EFO_0001779]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - experimental factor
    rank: 12
    is_a: investigation field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000008
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  fertilizer_regm:
    name: fertilizer_regm
    annotations:
      expected_value:
        tag: expected_value
        value: fertilizer name;fertilizer amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving the use of fertilizers; should
      include the name of fertilizer, amount administered, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple fertilizer
      regimens
    title: fertilizer regimen
    examples:
    - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - fertilizer regimen
    rank: 242
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000556
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  fungicide_regm:
    name: fungicide_regm
    annotations:
      expected_value:
        tag: expected_value
        value: fungicide name;fungicide amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of fungicides; should include
      the name of fungicide, amount administered, treatment regimen including how
      many times the treatment was repeated, how long each treatment lasted, and the
      start and end time of the entire treatment; can include multiple fungicide regimens
    title: fungicide regimen
    examples:
    - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - fungicide regimen
    rank: 243
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000557
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  gaseous_environment:
    name: gaseous_environment
    annotations:
      expected_value:
        tag: expected_value
        value: gaseous compound name;gaseous compound amount;treatment interval and
          duration
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: m
    description: Use of conditions with differing gaseous environments; should include
      the name of gaseous compound, amount administered, treatment duration, interval
      and total experimental duration; can include multiple gaseous environment regimens
    title: gaseous environment
    todos:
    - would like to see usage examples for this slot. Requiring micromole/L seems
      too limiting and doesn't match expected_value value
    - did I do this right? keep the example that's provided and add another? so as
      to not override
    - would like to see usage examples for this slot. Requiring micromole/L seems
      too limiting and doesn't match expected_value value
    - did I do this right? keep the example that's provided and add another? so as
      to not override
    examples:
    - value: CO2; 500ppm above ambient; constant
    - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gaseous environment
    rank: 20
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000558
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  genetic_mod:
    name: genetic_mod
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url or free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Genetic modifications of the genome of an organism, which may occur
      naturally by spontaneous mutation, or be introduced by some experimental means,
      e.g. specification of a transgene or the gene knocked-out or details of transient
      transfection
    title: genetic modification
    examples:
    - value: aox1A transgenic
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - genetic modification
    rank: 244
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0000859
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  geo_loc_name:
    name: geo_loc_name
    annotations:
      expected_value:
        tag: expected_value
        value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location
          name'
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name.
    title: geographic location (country and/or sea,region)
    examples:
    - value: 'USA: Maryland, Bethesda'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - geographic location (country and/or sea,region)
    rank: 4
    is_a: environment field
    string_serialization: '{text}: {text}, {text}'
    slot_uri: MIXS:0000010
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  gravity:
    name: gravity
    annotations:
      expected_value:
        tag: expected_value
        value: gravity factor value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: meter per square second, g
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of gravity factor to study
      various types of responses in presence, absence or modified levels of gravity;
      treatment regimen including how many times the treatment was repeated, how long
      each treatment lasted, and the start and end time of the entire treatment; can
      include multiple treatments
    title: gravity
    examples:
    - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gravity
    rank: 245
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000559
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  growth_facil:
    name: growth_facil
    annotations:
      expected_value:
        tag: expected_value
        value: free text or CO
      occurrence:
        tag: occurrence
        value: '1'
    description: 'Type of facility/location where the sample was harvested; controlled
      vocabulary: growth chamber, open top chamber, glasshouse, experimental garden,
      field.'
    title: growth facility
    notes:
    - 'Removed from description: Alternatively use Crop Ontology (CO) terms'
    examples:
    - value: Growth chamber [CO_715:0000189]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - growth facility
    rank: 1
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001043
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: GrowthFacilEnum
    required: true
    multivalued: false
  growth_habit:
    name: growth_habit
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Characteristic shape, appearance or growth form of a plant species
    title: growth habit
    examples:
    - value: spreading
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - growth habit
    rank: 246
    is_a: core field
    slot_uri: MIXS:0001044
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: growth_habit_enum
    multivalued: false
  growth_hormone_regm:
    name: growth_hormone_regm
    annotations:
      expected_value:
        tag: expected_value
        value: growth hormone name;growth hormone amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of growth hormones; should
      include the name of growth hormone, amount administered, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple growth
      hormone regimens
    title: growth hormone regimen
    examples:
    - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - growth hormone regimen
    rank: 247
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000560
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  herbicide_regm:
    name: herbicide_regm
    annotations:
      expected_value:
        tag: expected_value
        value: herbicide name;herbicide amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of herbicides; information
      about treatment involving use of growth hormones; should include the name of
      herbicide, amount administered, treatment regimen including how many times the
      treatment was repeated, how long each treatment lasted, and the start and end
      time of the entire treatment; can include multiple regimens
    title: herbicide regimen
    examples:
    - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - herbicide regimen
    rank: 248
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000561
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_age:
    name: host_age
    annotations:
      expected_value:
        tag: expected_value
        value: value
      preferred_unit:
        tag: preferred_unit
        value: year, day, hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Age of host at the time of sampling; relevant scale depends on species
      and study, e.g. Could be seconds for amoebae or centuries for trees
    title: host age
    examples:
    - value: 10 days
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host age
    rank: 249
    is_a: core field
    slot_uri: MIXS:0000255
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_common_name:
    name: host_common_name
    annotations:
      expected_value:
        tag: expected_value
        value: common name
      occurrence:
        tag: occurrence
        value: '1'
    description: Common name of the host.
    title: host common name
    examples:
    - value: human
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host common name
    rank: 250
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000248
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_disease_stat:
    name: host_disease_stat
    annotations:
      expected_value:
        tag: expected_value
        value: disease name or Disease Ontology term
    description: List of diseases with which the host has been diagnosed; can include
      multiple diagnoses. The value of the field depends on host; for humans the terms
      should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
      non-human host diseases are free text
    title: host disease status
    examples:
    - value: rabies [DOID:11260]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host disease status
    rank: 390
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000031
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_dry_mass:
    name: host_dry_mass
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: kilogram, gram
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of dry mass
    title: host dry mass
    examples:
    - value: 500 gram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host dry mass
    rank: 251
    is_a: core field
    slot_uri: MIXS:0000257
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_genotype:
    name: host_genotype
    annotations:
      expected_value:
        tag: expected_value
        value: genotype
      occurrence:
        tag: occurrence
        value: '1'
    description: Observed genotype
    title: host genotype
    examples:
    - value: C57BL/6
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host genotype
    rank: 252
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000365
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_height:
    name: host_height
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: centimeter, millimeter, meter
      occurrence:
        tag: occurrence
        value: '1'
    description: The height of subject
    title: host height
    examples:
    - value: 0.1 meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host height
    rank: 253
    is_a: core field
    slot_uri: MIXS:0000264
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_length:
    name: host_length
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: centimeter, millimeter, meter
      occurrence:
        tag: occurrence
        value: '1'
    description: The length of subject
    title: host length
    examples:
    - value: 1 meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host length
    rank: 254
    is_a: core field
    slot_uri: MIXS:0000256
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_life_stage:
    name: host_life_stage
    annotations:
      expected_value:
        tag: expected_value
        value: stage
      occurrence:
        tag: occurrence
        value: '1'
    description: Description of life stage of host
    title: host life stage
    examples:
    - value: adult
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host life stage
    rank: 255
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000251
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_phenotype:
    name: host_phenotype
    annotations:
      expected_value:
        tag: expected_value
        value: PATO or HP
      occurrence:
        tag: occurrence
        value: '1'
    description: Phenotype of human or other host. For phenotypic quality ontology
      (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato.
      For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP
    title: host phenotype
    examples:
    - value: elongated [PATO:0001154]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host phenotype
    rank: 256
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000874
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  host_subspecf_genlin:
    name: host_subspecf_genlin
    annotations:
      expected_value:
        tag: expected_value
        value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,
          e.g. serovar, biotype, ecotype, variety, cultivar.
      occurrence:
        tag: occurrence
        value: m
    description: Information about the genetic distinctness of the host organism below
      the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,
      or any relevant genetic typing schemes like Group I plasmid. Subspecies should
      not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage
      name and the lineage rank separated by a colon, e.g., biovar:abc123.
    title: host subspecific genetic lineage
    examples:
    - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host subspecific genetic lineage
    rank: 257
    is_a: core field
    string_serialization: '{rank name}:{text}'
    slot_uri: MIXS:0001318
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_symbiont:
    name: host_symbiont
    annotations:
      expected_value:
        tag: expected_value
        value: species name or common name
      occurrence:
        tag: occurrence
        value: m
    description: The taxonomic name of the organism(s) found living in mutualistic,
      commensalistic, or parasitic symbiosis with the specific host.
    title: observed host symbionts
    examples:
    - value: flukeworms
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - observed host symbionts
    rank: 258
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001298
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_taxid:
    name: host_taxid
    annotations:
      expected_value:
        tag: expected_value
        value: NCBI taxon identifier
      occurrence:
        tag: occurrence
        value: '1'
    description: NCBI taxon id of the host, e.g. 9606
    title: host taxid
    comments:
    - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host taxid
    rank: 259
    is_a: core field
    slot_uri: MIXS:0000250
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_tot_mass:
    name: host_tot_mass
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: kilogram, gram
      occurrence:
        tag: occurrence
        value: '1'
    description: Total mass of the host at collection, the unit depends on host
    title: host total mass
    examples:
    - value: 2500 gram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host total mass
    rank: 260
    is_a: core field
    slot_uri: MIXS:0000263
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_wet_mass:
    name: host_wet_mass
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: kilogram, gram
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of wet mass
    title: host wet mass
    examples:
    - value: 1500 gram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host wet mass
    rank: 261
    is_a: core field
    slot_uri: MIXS:0000567
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  humidity_regm:
    name: humidity_regm
    annotations:
      expected_value:
        tag: expected_value
        value: humidity value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram per cubic meter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to varying degree
      of humidity; information about treatment involving use of growth hormones; should
      include amount of humidity administered, treatment regimen including how many
      times the treatment was repeated, how long each treatment lasted, and the start
      and end time of the entire treatment; can include multiple regimens
    title: humidity regimen
    examples:
    - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - humidity regimen
    rank: 21
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000568
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  isotope_exposure:
    name: isotope_exposure
    description: List isotope exposure or addition applied to your sample.
    title: isotope exposure/addition
    todos:
    - Can we make the H218O correctly super and subscripted?
    comments:
    - This is required when your experimental design includes the use of isotopically
      labeled compounds
    examples:
    - value: 13C glucose
    - value: H218O
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000751
    rank: 16
    string_serialization: '{termLabel} {[termID]}; {timestamp}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
  lat_lon:
    name: lat_lon
    annotations:
      expected_value:
        tag: expected_value
        value: decimal degrees,  limit to 8 decimal points
    description: The geographical origin of the sample as defined by latitude and
      longitude. The values should be reported in decimal degrees and in WGS84 system
    title: geographic location (latitude and longitude)
    notes:
    - This is currently a required field but it's not clear if this should be required
      for human hosts
    examples:
    - value: 50.586825 6.408977
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - geographic location (latitude and longitude)
    rank: 5
    is_a: environment field
    string_serialization: '{lat lon}'
    slot_uri: MIXS:0000009
    owner: Biosample
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$
  light_regm:
    name: light_regm
    annotations:
      expected_value:
        tag: expected_value
        value: exposure type;light intensity;light quality
      preferred_unit:
        tag: preferred_unit
        value: lux; micrometer, nanometer, angstrom
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about treatment(s) involving exposure to light, including
      both light intensity and quality.
    title: light regimen
    examples:
    - value: incandescant light;10 lux;450 nanometer
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - light regimen
    rank: 24
    is_a: core field
    string_serialization: '{text};{float} {unit};{float} {unit}'
    slot_uri: MIXS:0000569
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      \S+$
  mechanical_damage:
    name: mechanical_damage
    annotations:
      expected_value:
        tag: expected_value
        value: damage type;body site
      occurrence:
        tag: occurrence
        value: m
    description: Information about any mechanical damage exerted on the plant; can
      include multiple damages and sites
    title: mechanical damage
    examples:
    - value: pruning;bark
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mechanical damage
    rank: 262
    is_a: core field
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0001052
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  mineral_nutr_regm:
    name: mineral_nutr_regm
    annotations:
      expected_value:
        tag: expected_value
        value: mineral nutrient name;mineral nutrient amount;treatment interval and
          duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving the use of mineral supplements;
      should include the name of mineral nutrient, amount administered, treatment
      regimen including how many times the treatment was repeated, how long each treatment
      lasted, and the start and end time of the entire treatment; can include multiple
      mineral nutrient regimens
    title: mineral nutrient regimen
    examples:
    - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mineral nutrient regimen
    rank: 263
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000570
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  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]+)$
  non_min_nutr_regm:
    name: non_min_nutr_regm
    annotations:
      expected_value:
        tag: expected_value
        value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval
          and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving the exposure of plant to non-mineral
      nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral
      nutrient, amount administered, treatment regimen including how many times the
      treatment was repeated, how long each treatment lasted, and the start and end
      time of the entire treatment; can include multiple non-mineral nutrient regimens
    title: non-mineral nutrient regimen
    examples:
    - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - non-mineral nutrient regimen
    rank: 264
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000571
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  organism_count:
    name: organism_count
    annotations:
      expected_value:
        tag: expected_value
        value: organism name;measurement value;enumeration
      preferred_unit:
        tag: preferred_unit
        value: number of cells per cubic meter, number of cells per milliliter, number
          of cells per cubic centimeter
      occurrence:
        tag: occurrence
        value: m
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organism count
    rank: 30
    is_a: core field
    slot_uri: MIXS:0000103
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$
  oxy_stat_samp:
    name: oxy_stat_samp
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Oxygenation status of sample
    title: oxygenation status of sample
    examples:
    - value: aerobic
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - oxygenation status of sample
    rank: 25
    is_a: core field
    slot_uri: MIXS:0000753
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: OxyStatSampEnum
    multivalued: false
  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
  pesticide_regm:
    name: pesticide_regm
    annotations:
      expected_value:
        tag: expected_value
        value: pesticide name;pesticide amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of insecticides; should
      include the name of pesticide, amount administered, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple pesticide
      regimens
    title: pesticide regimen
    examples:
    - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pesticide regimen
    rank: 265
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000573
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  ph_regm:
    name: ph_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving exposure of plants to varying
      levels of ph of the growth media, treatment regimen including how many times
      the treatment was repeated, how long each treatment lasted, and the start and
      end time of the entire treatment; can include multiple regimen
    title: pH regimen
    examples:
    - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pH regimen
    rank: 266
    is_a: core field
    string_serialization: '{float};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001056
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  plant_growth_med:
    name: plant_growth_med
    annotations:
      expected_value:
        tag: expected_value
        value: EO or enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Specification of the media for growing the plants or tissue cultured
      samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in
      vitro liquid culture medium. Recommended value is a specific value from EO:plant
      growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147)
      or other controlled vocabulary
    title: plant growth medium
    examples:
    - value: hydroponic plant culture media [EO:0007067]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - plant growth medium
    rank: 267
    is_a: core field
    slot_uri: MIXS:0001057
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  plant_product:
    name: plant_product
    annotations:
      expected_value:
        tag: expected_value
        value: product name
      occurrence:
        tag: occurrence
        value: '1'
    description: Substance produced by the plant, where the sample was obtained from
    title: plant product
    examples:
    - value: xylem sap [PO:0025539]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - plant product
    rank: 268
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001058
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  plant_sex:
    name: plant_sex
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Sex of the reproductive parts on the whole plant, e.g. pistillate,
      staminate, monoecieous, hermaphrodite.
    title: plant sex
    examples:
    - value: Hermaphroditic
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - plant sex
    rank: 269
    is_a: core field
    slot_uri: MIXS:0001059
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: plant_sex_enum
    multivalued: false
  plant_struc:
    name: plant_struc
    annotations:
      expected_value:
        tag: expected_value
        value: PO
      occurrence:
        tag: occurrence
        value: '1'
    description: Name of plant structure the sample was obtained from; for Plant Ontology
      (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,
      e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the
      sex of it can be recorded here.
    title: plant structure
    examples:
    - value: epidermis [PO:0005679]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - plant structure
    rank: 270
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001060
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  radiation_regm:
    name: radiation_regm
    annotations:
      expected_value:
        tag: expected_value
        value: radiation type name;radiation amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: rad, gray
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving exposure of plant or a plant
      part to a particular radiation regimen; should include the radiation type, amount
      or intensity administered, treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment; can include multiple radiation regimens
    title: radiation regimen
    examples:
    - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - radiation regimen
    rank: 271
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000575
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  rainfall_regm:
    name: rainfall_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: millimeter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to a given amount
      of rainfall, treatment regimen including how many times the treatment was repeated,
      how long each treatment lasted, and the start and end time of the entire treatment;
      can include multiple regimens
    title: rainfall regimen
    examples:
    - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rainfall regimen
    rank: 272
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000576
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  root_cond:
    name: root_cond
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url or free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Relevant rooting conditions such as field plot size, sowing density,
      container dimensions, number of plants per container.
    title: rooting conditions
    examples:
    - value: http://himedialabs.com/TD/PT158.pdf
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting conditions
    rank: 273
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001061
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  root_med_carbon:
    name: root_med_carbon
    annotations:
      expected_value:
        tag: expected_value
        value: carbon source name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Source of organic carbon in the culture rooting medium; e.g. sucrose.
    title: rooting medium carbon
    examples:
    - value: sucrose
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium carbon
    rank: 274
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000577
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  root_med_macronutr:
    name: root_med_macronutr
    annotations:
      expected_value:
        tag: expected_value
        value: macronutrient name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of the culture rooting medium macronutrients (N,P, K,
      Ca, Mg, S); e.g. KH2PO4 (170 mg/L).
    title: rooting medium macronutrients
    examples:
    - value: KH2PO4;170 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium macronutrients
    rank: 275
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000578
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  root_med_micronutr:
    name: root_med_micronutr
    annotations:
      expected_value:
        tag: expected_value
        value: micronutrient name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of the culture rooting medium micronutrients (Fe, Mn,
      Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L).
    title: rooting medium micronutrients
    examples:
    - value: H3BO3;6.2 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium micronutrients
    rank: 276
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000579
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  root_med_ph:
    name: root_med_ph
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    description: pH measurement of the culture rooting medium; e.g. 5.5.
    title: rooting medium pH
    examples:
    - value: '7.5'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium pH
    rank: 277
    is_a: core field
    slot_uri: MIXS:0001062
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  root_med_regl:
    name: root_med_regl
    annotations:
      expected_value:
        tag: expected_value
        value: regulator name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Growth regulators in the culture rooting medium such as cytokinins,
      auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA.
    title: rooting medium regulators
    examples:
    - value: abscisic acid;0.75 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium regulators
    rank: 278
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000581
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  root_med_solid:
    name: root_med_solid
    annotations:
      expected_value:
        tag: expected_value
        value: name
      occurrence:
        tag: occurrence
        value: '1'
    description: Specification of the solidifying agent in the culture rooting medium;
      e.g. agar.
    title: rooting medium solidifier
    examples:
    - value: agar
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium solidifier
    rank: 279
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001063
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  root_med_suppl:
    name: root_med_suppl
    annotations:
      expected_value:
        tag: expected_value
        value: supplement name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Organic supplements of the culture rooting medium, such as vitamins,
      amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid
      (0.5 mg/L).
    title: rooting medium organic supplements
    examples:
    - value: nicotinic acid;0.5 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium organic supplements
    rank: 280
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000580
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  salinity:
    name: salinity
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: practical salinity unit, percentage
      occurrence:
        tag: occurrence
        value: '1'
    description: The total concentration of all dissolved salts in a liquid or solid
      sample. While salinity can be measured by a complete chemical analysis, this
      method is difficult and time consuming. More often, it is instead derived from
      the conductivity measurement. This is known as practical salinity. These derivations
      compare the specific conductance of the sample to a salinity standard such as
      seawater.
    title: salinity
    examples:
    - value: 25 practical salinity unit
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - salinity
    rank: 54
    is_a: core field
    slot_uri: MIXS:0000183
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  salinity_meth:
    name: salinity_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining salinity
    title: salinity method
    examples:
    - value: https://doi.org/10.1007/978-1-61779-986-0_28
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - salinity method
    rank: 55
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000341
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  salt_regm:
    name: salt_regm
    annotations:
      expected_value:
        tag: expected_value
        value: salt name;salt amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, microgram, mole per liter, gram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of salts as supplement
      to liquid and soil growth media; should include the name of salt, amount administered,
      treatment regimen including how many times the treatment was repeated, how long
      each treatment lasted, and the start and end time of the entire treatment; can
      include multiple salt regimens
    title: salt regimen
    examples:
    - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - salt regimen
    rank: 281
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000582
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  samp_capt_status:
    name: samp_capt_status
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Reason for the sample
    title: sample capture status
    examples:
    - value: farm sample
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample capture status
    rank: 282
    is_a: core field
    slot_uri: MIXS:0000860
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: samp_capt_status_enum
    multivalued: false
  samp_collec_device:
    name: samp_collec_device
    annotations:
      expected_value:
        tag: expected_value
        value: device name
    description: The device used to collect an environmental sample. This field accepts
      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
    title: sample collection device
    comments:
    - Report dimensions and details when applicable
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample collection device
    rank: 14
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000002
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  samp_collec_method:
    name: samp_collec_method
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url , or text
    description: The method employed for collecting the sample.
    title: sample collection method
    comments:
    - This can be a citation or description
    examples:
    - value: swabbing
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample collection method
    rank: 15
    is_a: nucleic acid sequence source field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001225
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
  samp_dis_stage:
    name: samp_dis_stage
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Stage of the disease at the time of sample collection, e.g. inoculation,
      penetration, infection, growth and reproduction, dissemination of pathogen.
    title: sample disease stage
    examples:
    - value: infection
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample disease stage
    rank: 283
    is_a: core field
    slot_uri: MIXS:0000249
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: samp_dis_stage_enum
    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]+'
  season_environment:
    name: season_environment
    annotations:
      expected_value:
        tag: expected_value
        value: seasonal environment name;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Treatment involving an exposure to a particular season (e.g. Winter,
      summer, rabi, rainy etc.), treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment
    title: seasonal environment
    examples:
    - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - seasonal environment
    rank: 284
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001068
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    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
  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
  standing_water_regm:
    name: standing_water_regm
    annotations:
      expected_value:
        tag: expected_value
        value: standing water type;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Treatment involving an exposure to standing water during a plant's
      life span, types can be flood water or standing water, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple regimens
    title: standing water regimen
    examples:
    - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - standing water regimen
    rank: 286
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001069
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  start_date_inc:
    name: start_date_inc
    description: Date the incubation was started. Only relevant for incubation samples.
    title: incubation start date
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
      date only
    comments:
    - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
      are all acceptable.
    examples:
    - value: 2021-04-15, 2021-04 and 2021 are all acceptable.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 4
    string_serialization: '{date, arbitrary precision}'
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  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.*$
  tiss_cult_growth_med:
    name: tiss_cult_growth_med
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url or free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Description of plant tissue culture growth media used
    title: tissue culture growth media
    examples:
    - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - tissue culture growth media
    rank: 287
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001070
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  water_temp_regm:
    name: water_temp_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to water with varying
      degree of temperature, treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment; can include multiple regimens
    title: water temperature regimen
    examples:
    - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - water temperature regimen
    rank: 288
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000590
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  watering_regm:
    name: watering_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: milliliter, liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to watering frequencies,
      treatment regimen including how many times the treatment was repeated, how long
      each treatment lasted, and the start and end time of the entire treatment; can
      include multiple regimens
    title: watering regimen
    examples:
    - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    - value: 75% water holding capacity; constant
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - watering regimen
    rank: 25
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000591
    owner: Biosample
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  horizon_meth:
    name: horizon_meth
    title: horizon method
attributes:
  air_temp_regm:
    name: air_temp_regm
    annotations:
      expected_value:
        tag: expected_value
        value: temperature value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: meter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to varying temperatures;
      should include the temperature, treatment regimen including how many times the
      treatment was repeated, how long each treatment lasted, and the start and end
      time of the entire treatment; can include different temperature regimens
    title: air temperature regimen
    examples:
    - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - air temperature regimen
    rank: 16
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000551
    alias: air_temp_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  ances_data:
    name: ances_data
    annotations:
      expected_value:
        tag: expected_value
        value: free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about either pedigree or other ancestral information
      description (e.g. parental variety in case of mutant or selection), e.g. A/3*B
      (meaning [(A x B) x B] x B)
    title: ancestral data
    examples:
    - value: A/3*B
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - ancestral data
    rank: 237
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000247
    alias: ances_data
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  antibiotic_regm:
    name: antibiotic_regm
    annotations:
      expected_value:
        tag: expected_value
        value: antibiotic name;antibiotic amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: milligram
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving antibiotic administration;
      should include the name of antibiotic, amount administered, treatment regimen
      including how many times the treatment was repeated, how long each treatment
      lasted, and the start and end time of the entire treatment; can include multiple
      antibiotic regimens
    title: antibiotic regimen
    examples:
    - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - antibiotic regimen
    rank: 238
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000553
    alias: antibiotic_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  biol_stat:
    name: biol_stat
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: The level of genome modification.
    title: biological status
    examples:
    - value: natural
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - biological status
    rank: 239
    is_a: core field
    slot_uri: MIXS:0000858
    alias: biol_stat
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: biol_stat_enum
    multivalued: false
  biotic_regm:
    name: biotic_regm
    annotations:
      expected_value:
        tag: expected_value
        value: free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about treatment(s) involving use of biotic factors, such
      as bacteria, viruses or fungi.
    title: biotic regimen
    examples:
    - value: sample inoculated with Rhizobium spp. Culture
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - biotic regimen
    rank: 13
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001038
    alias: biotic_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  biotic_relationship:
    name: biotic_relationship
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
    description: Description of relationship(s) between the subject organism and other
      organism(s) it is associated with. E.g., parasite on species X; mutualist with
      species Y. The target organism is the subject of the relationship, and the other
      organism(s) is the object
    title: observed biotic relationship
    examples:
    - value: free living
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - observed biotic relationship
    rank: 22
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000028
    alias: biotic_relationship
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: biotic_relationship_enum
    multivalued: false
  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: PlantAssociatedInterface
    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_mutagen:
    name: chem_mutagen
    annotations:
      expected_value:
        tag: expected_value
        value: mutagen name;mutagen amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Treatment involving use of mutagens; should include the name of mutagen,
      amount administered, treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment; can include multiple mutagen regimens
    title: chemical mutagen
    examples:
    - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chemical mutagen
    rank: 240
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000555
    alias: chem_mutagen
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  climate_environment:
    name: climate_environment
    annotations:
      expected_value:
        tag: expected_value
        value: climate name;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Treatment involving an exposure to a particular climate; treatment
      regimen including how many times the treatment was repeated, how long each treatment
      lasted, and the start and end time of the entire treatment; can include multiple
      climates
    title: climate environment
    todos:
    - description says "can include multiple climates" but multivalued is set to false
    - add examples, i need to see some examples to add correctly formatted example.
    - description says "can include multiple climates" but multivalued is set to false
    - add examples, i need to see some examples to add correctly formatted example.
    examples:
    - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - climate environment
    rank: 19
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001040
    alias: climate_environment
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  collection_date:
    name: collection_date
    annotations:
      expected_value:
        tag: expected_value
        value: date and time
    description: The date of sampling
    title: collection date
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only
    - Use modified term (amended definition)
    examples:
    - value: '2021-04-15'
    - value: 2021-04
    - value: '2021'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - collection date
    rank: 3
    is_a: environment field
    string_serialization: '{date, arbitrary precision}'
    slot_uri: MIXS:0000011
    alias: collection_date
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  collection_date_inc:
    name: collection_date_inc
    description: Date the incubation was harvested/collected/ended. Only relevant
      for incubation samples.
    title: incubation collection date
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
      date only
    comments:
    - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
      are all acceptable.
    examples:
    - value: 2021-04-15, 2021-04 and 2021 are all acceptable.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 2
    string_serialization: '{date, arbitrary precision}'
    alias: collection_date_inc
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  collection_time:
    name: collection_time
    description: The time of sampling, either as an instance (single point) or interval.
    title: collection time, GMT
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
      time only
    comments:
    - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
    examples:
    - value: 13:33 or 13:33:55
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 1
    string_serialization: '{time, seconds optional}'
    alias: collection_time
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
  cult_root_med:
    name: cult_root_med
    annotations:
      expected_value:
        tag: expected_value
        value: name, PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Name or reference for the hydroponic or in vitro culture rooting
      medium; can be the name of a commonly used medium or reference to a specific
      medium, e.g. Murashige and Skoog medium. If the medium has not been formally
      published, use the rooting medium descriptors.
    title: culture rooting medium
    examples:
    - value: http://himedialabs.com/TD/PT158.pdf
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - culture rooting medium
    rank: 241
    is_a: core field
    string_serialization: '{text}|{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0001041
    alias: cult_root_med
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  depth:
    name: depth
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: The vertical distance below local surface, e.g. for sediment or soil
      samples depth is measured from sediment or soil surface, respectively. Depth
      can be reported as an interval for subsurface samples.
    title: depth, meters
    notes:
    - Use modified term
    comments:
    - All depths must be reported in meters. Provide the numerical portion only.
    examples:
    - value: 0 - 0.1
    - value: '1'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - depth
    rank: 9
    is_a: environment field
    string_serialization: '{float}|{float}-{float}'
    slot_uri: MIXS:0000018
    alias: depth
    owner: PlantAssociatedInterface
    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: PlantAssociatedInterface
    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: PlantAssociatedInterface
    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: PlantAssociatedInterface
    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: PlantAssociatedInterface
    domain_of:
    - Biosample
    - Study
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: EcosystemTypeEnum
    recommended: true
  elev:
    name: elev
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit.
    title: elevation, meters
    comments:
    - All elevations must be reported in meters. Provide the numerical portion only.
    - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,
      if needed, to help estimate the elevation based on latitude and longitude coordinates.
    examples:
    - value: '225'
    - value: '0'
    - value: '1250'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - elevation
    rank: 6
    is_a: environment field
    slot_uri: MIXS:0000093
    alias: elev
    owner: PlantAssociatedInterface
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: float
    required: true
    multivalued: false
  env_broad_scale:
    name: env_broad_scale
    annotations:
      expected_value:
        tag: expected_value
        value: The major environment type(s) where the sample was collected. Recommend
          subclasses of biome [ENVO:00000428]. Multiple terms can be separated by
          one or more pipes.
      tooltip:
        tag: tooltip
        value: The biome or major environmental system where the sample or specimen
          originated. Choose values from subclasses of the 'biome' class [ENVO:00000428]
          in the Environment Ontology (ENVO). For host-associated or plant-associated
          samples, use terms from the UBERON or Plant Ontology to describe the broad
          anatomical or morphological context
    description: 'In this field, report which major environmental system your sample
      or specimen came from. The systems identified should have a coarse spatial grain,
      to provide the general environmental context of where the sampling was done
      (e.g. were you in the desert or a rainforest?). We recommend using subclasses
      of ENVO''s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format
      (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel
      [termID]|termLabel [termID]. Example: Annotating a water sample from the photic
      zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome
      [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider:
      tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new
      terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html'
    title: broad-scale environmental context
    notes:
    - range changed to enumeration late in makefile, so this is modified (but "sample
      ID" anyway)
    examples:
    - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water
        sample from the photic zone in middle of the Atlantic Ocean
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - broad-scale environmental context
    rank: 6
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    alias: env_broad_scale
    owner: PlantAssociatedInterface
    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: PlantAssociatedInterface
    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: PlantAssociatedInterface
    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: PlantAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  fertilizer_regm:
    name: fertilizer_regm
    annotations:
      expected_value:
        tag: expected_value
        value: fertilizer name;fertilizer amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving the use of fertilizers; should
      include the name of fertilizer, amount administered, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple fertilizer
      regimens
    title: fertilizer regimen
    examples:
    - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - fertilizer regimen
    rank: 242
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000556
    alias: fertilizer_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  fungicide_regm:
    name: fungicide_regm
    annotations:
      expected_value:
        tag: expected_value
        value: fungicide name;fungicide amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of fungicides; should include
      the name of fungicide, amount administered, treatment regimen including how
      many times the treatment was repeated, how long each treatment lasted, and the
      start and end time of the entire treatment; can include multiple fungicide regimens
    title: fungicide regimen
    examples:
    - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - fungicide regimen
    rank: 243
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000557
    alias: fungicide_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  gaseous_environment:
    name: gaseous_environment
    annotations:
      expected_value:
        tag: expected_value
        value: gaseous compound name;gaseous compound amount;treatment interval and
          duration
      preferred_unit:
        tag: preferred_unit
        value: micromole per liter
      occurrence:
        tag: occurrence
        value: m
    description: Use of conditions with differing gaseous environments; should include
      the name of gaseous compound, amount administered, treatment duration, interval
      and total experimental duration; can include multiple gaseous environment regimens
    title: gaseous environment
    todos:
    - would like to see usage examples for this slot. Requiring micromole/L seems
      too limiting and doesn't match expected_value value
    - did I do this right? keep the example that's provided and add another? so as
      to not override
    - would like to see usage examples for this slot. Requiring micromole/L seems
      too limiting and doesn't match expected_value value
    - did I do this right? keep the example that's provided and add another? so as
      to not override
    examples:
    - value: CO2; 500ppm above ambient; constant
    - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gaseous environment
    rank: 20
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000558
    alias: gaseous_environment
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  genetic_mod:
    name: genetic_mod
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url or free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Genetic modifications of the genome of an organism, which may occur
      naturally by spontaneous mutation, or be introduced by some experimental means,
      e.g. specification of a transgene or the gene knocked-out or details of transient
      transfection
    title: genetic modification
    examples:
    - value: aox1A transgenic
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - genetic modification
    rank: 244
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0000859
    alias: genetic_mod
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  geo_loc_name:
    name: geo_loc_name
    annotations:
      expected_value:
        tag: expected_value
        value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location
          name'
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name.
    title: geographic location (country and/or sea,region)
    examples:
    - value: 'USA: Maryland, Bethesda'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - geographic location (country and/or sea,region)
    rank: 4
    is_a: environment field
    string_serialization: '{text}: {text}, {text}'
    slot_uri: MIXS:0000010
    alias: geo_loc_name
    owner: PlantAssociatedInterface
    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: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  gravity:
    name: gravity
    annotations:
      expected_value:
        tag: expected_value
        value: gravity factor value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: meter per square second, g
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of gravity factor to study
      various types of responses in presence, absence or modified levels of gravity;
      treatment regimen including how many times the treatment was repeated, how long
      each treatment lasted, and the start and end time of the entire treatment; can
      include multiple treatments
    title: gravity
    examples:
    - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gravity
    rank: 245
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000559
    alias: gravity
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  growth_facil:
    name: growth_facil
    annotations:
      expected_value:
        tag: expected_value
        value: free text or CO
      occurrence:
        tag: occurrence
        value: '1'
    description: 'Type of facility/location where the sample was harvested; controlled
      vocabulary: growth chamber, open top chamber, glasshouse, experimental garden,
      field.'
    title: growth facility
    notes:
    - 'Removed from description: Alternatively use Crop Ontology (CO) terms'
    examples:
    - value: Growth chamber [CO_715:0000189]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - growth facility
    rank: 1
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001043
    alias: growth_facil
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SoilInterface
    slot_group: mixs_modified_section
    range: GrowthFacilEnum
    required: true
    multivalued: false
  growth_habit:
    name: growth_habit
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Characteristic shape, appearance or growth form of a plant species
    title: growth habit
    examples:
    - value: spreading
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - growth habit
    rank: 246
    is_a: core field
    slot_uri: MIXS:0001044
    alias: growth_habit
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: growth_habit_enum
    multivalued: false
  growth_hormone_regm:
    name: growth_hormone_regm
    annotations:
      expected_value:
        tag: expected_value
        value: growth hormone name;growth hormone amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of growth hormones; should
      include the name of growth hormone, amount administered, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple growth
      hormone regimens
    title: growth hormone regimen
    examples:
    - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - growth hormone regimen
    rank: 247
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000560
    alias: growth_hormone_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  herbicide_regm:
    name: herbicide_regm
    annotations:
      expected_value:
        tag: expected_value
        value: herbicide name;herbicide amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of herbicides; information
      about treatment involving use of growth hormones; should include the name of
      herbicide, amount administered, treatment regimen including how many times the
      treatment was repeated, how long each treatment lasted, and the start and end
      time of the entire treatment; can include multiple regimens
    title: herbicide regimen
    examples:
    - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - herbicide regimen
    rank: 248
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000561
    alias: herbicide_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_age:
    name: host_age
    annotations:
      expected_value:
        tag: expected_value
        value: value
      preferred_unit:
        tag: preferred_unit
        value: year, day, hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Age of host at the time of sampling; relevant scale depends on species
      and study, e.g. Could be seconds for amoebae or centuries for trees
    title: host age
    examples:
    - value: 10 days
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host age
    rank: 249
    is_a: core field
    slot_uri: MIXS:0000255
    alias: host_age
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_common_name:
    name: host_common_name
    annotations:
      expected_value:
        tag: expected_value
        value: common name
      occurrence:
        tag: occurrence
        value: '1'
    description: Common name of the host.
    title: host common name
    examples:
    - value: human
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host common name
    rank: 250
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000248
    alias: host_common_name
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_disease_stat:
    name: host_disease_stat
    annotations:
      expected_value:
        tag: expected_value
        value: disease name or Disease Ontology term
    description: List of diseases with which the host has been diagnosed; can include
      multiple diagnoses. The value of the field depends on host; for humans the terms
      should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
      non-human host diseases are free text
    title: host disease status
    examples:
    - value: rabies [DOID:11260]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host disease status
    rank: 390
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000031
    alias: host_disease_stat
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_dry_mass:
    name: host_dry_mass
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: kilogram, gram
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of dry mass
    title: host dry mass
    examples:
    - value: 500 gram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host dry mass
    rank: 251
    is_a: core field
    slot_uri: MIXS:0000257
    alias: host_dry_mass
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_genotype:
    name: host_genotype
    annotations:
      expected_value:
        tag: expected_value
        value: genotype
      occurrence:
        tag: occurrence
        value: '1'
    description: Observed genotype
    title: host genotype
    examples:
    - value: C57BL/6
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host genotype
    rank: 252
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000365
    alias: host_genotype
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_height:
    name: host_height
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: centimeter, millimeter, meter
      occurrence:
        tag: occurrence
        value: '1'
    description: The height of subject
    title: host height
    examples:
    - value: 0.1 meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host height
    rank: 253
    is_a: core field
    slot_uri: MIXS:0000264
    alias: host_height
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_length:
    name: host_length
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: centimeter, millimeter, meter
      occurrence:
        tag: occurrence
        value: '1'
    description: The length of subject
    title: host length
    examples:
    - value: 1 meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host length
    rank: 254
    is_a: core field
    slot_uri: MIXS:0000256
    alias: host_length
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_life_stage:
    name: host_life_stage
    annotations:
      expected_value:
        tag: expected_value
        value: stage
      occurrence:
        tag: occurrence
        value: '1'
    description: Description of life stage of host
    title: host life stage
    examples:
    - value: adult
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host life stage
    rank: 255
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000251
    alias: host_life_stage
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_phenotype:
    name: host_phenotype
    annotations:
      expected_value:
        tag: expected_value
        value: PATO or HP
      occurrence:
        tag: occurrence
        value: '1'
    description: Phenotype of human or other host. For phenotypic quality ontology
      (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato.
      For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP
    title: host phenotype
    examples:
    - value: elongated [PATO:0001154]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host phenotype
    rank: 256
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000874
    alias: host_phenotype
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  host_subspecf_genlin:
    name: host_subspecf_genlin
    annotations:
      expected_value:
        tag: expected_value
        value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,
          e.g. serovar, biotype, ecotype, variety, cultivar.
      occurrence:
        tag: occurrence
        value: m
    description: Information about the genetic distinctness of the host organism below
      the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,
      or any relevant genetic typing schemes like Group I plasmid. Subspecies should
      not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage
      name and the lineage rank separated by a colon, e.g., biovar:abc123.
    title: host subspecific genetic lineage
    examples:
    - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host subspecific genetic lineage
    rank: 257
    is_a: core field
    string_serialization: '{rank name}:{text}'
    slot_uri: MIXS:0001318
    alias: host_subspecf_genlin
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_symbiont:
    name: host_symbiont
    annotations:
      expected_value:
        tag: expected_value
        value: species name or common name
      occurrence:
        tag: occurrence
        value: m
    description: The taxonomic name of the organism(s) found living in mutualistic,
      commensalistic, or parasitic symbiosis with the specific host.
    title: observed host symbionts
    examples:
    - value: flukeworms
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - observed host symbionts
    rank: 258
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001298
    alias: host_symbiont
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_taxid:
    name: host_taxid
    annotations:
      expected_value:
        tag: expected_value
        value: NCBI taxon identifier
      occurrence:
        tag: occurrence
        value: '1'
    description: NCBI taxon id of the host, e.g. 9606
    title: host taxid
    comments:
    - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host taxid
    rank: 259
    is_a: core field
    slot_uri: MIXS:0000250
    alias: host_taxid
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  host_tot_mass:
    name: host_tot_mass
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: kilogram, gram
      occurrence:
        tag: occurrence
        value: '1'
    description: Total mass of the host at collection, the unit depends on host
    title: host total mass
    examples:
    - value: 2500 gram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host total mass
    rank: 260
    is_a: core field
    slot_uri: MIXS:0000263
    alias: host_tot_mass
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_wet_mass:
    name: host_wet_mass
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: kilogram, gram
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of wet mass
    title: host wet mass
    examples:
    - value: 1500 gram
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host wet mass
    rank: 261
    is_a: core field
    slot_uri: MIXS:0000567
    alias: host_wet_mass
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  humidity_regm:
    name: humidity_regm
    annotations:
      expected_value:
        tag: expected_value
        value: humidity value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram per cubic meter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to varying degree
      of humidity; information about treatment involving use of growth hormones; should
      include amount of humidity administered, treatment regimen including how many
      times the treatment was repeated, how long each treatment lasted, and the start
      and end time of the entire treatment; can include multiple regimens
    title: humidity regimen
    examples:
    - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - humidity regimen
    rank: 21
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000568
    alias: humidity_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
  isotope_exposure:
    name: isotope_exposure
    description: List isotope exposure or addition applied to your sample.
    title: isotope exposure/addition
    todos:
    - Can we make the H218O correctly super and subscripted?
    comments:
    - This is required when your experimental design includes the use of isotopically
      labeled compounds
    examples:
    - value: 13C glucose
    - value: H218O
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000751
    rank: 16
    string_serialization: '{termLabel} {[termID]}; {timestamp}'
    alias: isotope_exposure
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
  lat_lon:
    name: lat_lon
    annotations:
      expected_value:
        tag: expected_value
        value: decimal degrees,  limit to 8 decimal points
    description: The geographical origin of the sample as defined by latitude and
      longitude. The values should be reported in decimal degrees and in WGS84 system
    title: geographic location (latitude and longitude)
    notes:
    - This is currently a required field but it's not clear if this should be required
      for human hosts
    examples:
    - value: 50.586825 6.408977
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - geographic location (latitude and longitude)
    rank: 5
    is_a: environment field
    string_serialization: '{lat lon}'
    slot_uri: MIXS:0000009
    alias: lat_lon
    owner: PlantAssociatedInterface
    domain_of:
    - FieldResearchSite
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    multivalued: false
    pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$
  light_regm:
    name: light_regm
    annotations:
      expected_value:
        tag: expected_value
        value: exposure type;light intensity;light quality
      preferred_unit:
        tag: preferred_unit
        value: lux; micrometer, nanometer, angstrom
      occurrence:
        tag: occurrence
        value: '1'
    description: Information about treatment(s) involving exposure to light, including
      both light intensity and quality.
    title: light regimen
    examples:
    - value: incandescant light;10 lux;450 nanometer
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - light regimen
    rank: 24
    is_a: core field
    string_serialization: '{text};{float} {unit};{float} {unit}'
    slot_uri: MIXS:0000569
    alias: light_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      \S+$
  mechanical_damage:
    name: mechanical_damage
    annotations:
      expected_value:
        tag: expected_value
        value: damage type;body site
      occurrence:
        tag: occurrence
        value: m
    description: Information about any mechanical damage exerted on the plant; can
      include multiple damages and sites
    title: mechanical damage
    examples:
    - value: pruning;bark
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mechanical damage
    rank: 262
    is_a: core field
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0001052
    alias: mechanical_damage
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  mineral_nutr_regm:
    name: mineral_nutr_regm
    annotations:
      expected_value:
        tag: expected_value
        value: mineral nutrient name;mineral nutrient amount;treatment interval and
          duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving the use of mineral supplements;
      should include the name of mineral nutrient, amount administered, treatment
      regimen including how many times the treatment was repeated, how long each treatment
      lasted, and the start and end time of the entire treatment; can include multiple
      mineral nutrient regimens
    title: mineral nutrient regimen
    examples:
    - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - mineral nutrient regimen
    rank: 263
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000570
    alias: mineral_nutr_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  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: PlantAssociatedInterface
    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]+)$
  non_min_nutr_regm:
    name: non_min_nutr_regm
    annotations:
      expected_value:
        tag: expected_value
        value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval
          and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving the exposure of plant to non-mineral
      nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral
      nutrient, amount administered, treatment regimen including how many times the
      treatment was repeated, how long each treatment lasted, and the start and end
      time of the entire treatment; can include multiple non-mineral nutrient regimens
    title: non-mineral nutrient regimen
    examples:
    - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - non-mineral nutrient regimen
    rank: 264
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000571
    alias: non_min_nutr_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  organism_count:
    name: organism_count
    annotations:
      expected_value:
        tag: expected_value
        value: organism name;measurement value;enumeration
      preferred_unit:
        tag: preferred_unit
        value: number of cells per cubic meter, number of cells per milliliter, number
          of cells per cubic centimeter
      occurrence:
        tag: occurrence
        value: m
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organism count
    rank: 30
    is_a: core field
    slot_uri: MIXS:0000103
    alias: organism_count
    owner: PlantAssociatedInterface
    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: PlantAssociatedInterface
    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: PlantAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  pesticide_regm:
    name: pesticide_regm
    annotations:
      expected_value:
        tag: expected_value
        value: pesticide name;pesticide amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, mole per liter, milligram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of insecticides; should
      include the name of pesticide, amount administered, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple pesticide
      regimens
    title: pesticide regimen
    examples:
    - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pesticide regimen
    rank: 265
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000573
    alias: pesticide_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  ph_regm:
    name: ph_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving exposure of plants to varying
      levels of ph of the growth media, treatment regimen including how many times
      the treatment was repeated, how long each treatment lasted, and the start and
      end time of the entire treatment; can include multiple regimen
    title: pH regimen
    examples:
    - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - pH regimen
    rank: 266
    is_a: core field
    string_serialization: '{float};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001056
    alias: ph_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  plant_growth_med:
    name: plant_growth_med
    annotations:
      expected_value:
        tag: expected_value
        value: EO or enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Specification of the media for growing the plants or tissue cultured
      samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in
      vitro liquid culture medium. Recommended value is a specific value from EO:plant
      growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147)
      or other controlled vocabulary
    title: plant growth medium
    examples:
    - value: hydroponic plant culture media [EO:0007067]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - plant growth medium
    rank: 267
    is_a: core field
    slot_uri: MIXS:0001057
    alias: plant_growth_med
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  plant_product:
    name: plant_product
    annotations:
      expected_value:
        tag: expected_value
        value: product name
      occurrence:
        tag: occurrence
        value: '1'
    description: Substance produced by the plant, where the sample was obtained from
    title: plant product
    examples:
    - value: xylem sap [PO:0025539]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - plant product
    rank: 268
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001058
    alias: plant_product
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  plant_sex:
    name: plant_sex
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Sex of the reproductive parts on the whole plant, e.g. pistillate,
      staminate, monoecieous, hermaphrodite.
    title: plant sex
    examples:
    - value: Hermaphroditic
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - plant sex
    rank: 269
    is_a: core field
    slot_uri: MIXS:0001059
    alias: plant_sex
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: plant_sex_enum
    multivalued: false
  plant_struc:
    name: plant_struc
    annotations:
      expected_value:
        tag: expected_value
        value: PO
      occurrence:
        tag: occurrence
        value: '1'
    description: Name of plant structure the sample was obtained from; for Plant Ontology
      (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,
      e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the
      sex of it can be recorded here.
    title: plant structure
    examples:
    - value: epidermis [PO:0005679]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - plant structure
    rank: 270
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001060
    alias: plant_struc
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  radiation_regm:
    name: radiation_regm
    annotations:
      expected_value:
        tag: expected_value
        value: radiation type name;radiation amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: rad, gray
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving exposure of plant or a plant
      part to a particular radiation regimen; should include the radiation type, amount
      or intensity administered, treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment; can include multiple radiation regimens
    title: radiation regimen
    examples:
    - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - radiation regimen
    rank: 271
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000575
    alias: radiation_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  rainfall_regm:
    name: rainfall_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: millimeter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to a given amount
      of rainfall, treatment regimen including how many times the treatment was repeated,
      how long each treatment lasted, and the start and end time of the entire treatment;
      can include multiple regimens
    title: rainfall regimen
    examples:
    - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rainfall regimen
    rank: 272
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000576
    alias: rainfall_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  root_cond:
    name: root_cond
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url or free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Relevant rooting conditions such as field plot size, sowing density,
      container dimensions, number of plants per container.
    title: rooting conditions
    examples:
    - value: http://himedialabs.com/TD/PT158.pdf
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting conditions
    rank: 273
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001061
    alias: root_cond
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  root_med_carbon:
    name: root_med_carbon
    annotations:
      expected_value:
        tag: expected_value
        value: carbon source name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Source of organic carbon in the culture rooting medium; e.g. sucrose.
    title: rooting medium carbon
    examples:
    - value: sucrose
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium carbon
    rank: 274
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000577
    alias: root_med_carbon
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  root_med_macronutr:
    name: root_med_macronutr
    annotations:
      expected_value:
        tag: expected_value
        value: macronutrient name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of the culture rooting medium macronutrients (N,P, K,
      Ca, Mg, S); e.g. KH2PO4 (170 mg/L).
    title: rooting medium macronutrients
    examples:
    - value: KH2PO4;170 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium macronutrients
    rank: 275
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000578
    alias: root_med_macronutr
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  root_med_micronutr:
    name: root_med_micronutr
    annotations:
      expected_value:
        tag: expected_value
        value: micronutrient name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Measurement of the culture rooting medium micronutrients (Fe, Mn,
      Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L).
    title: rooting medium micronutrients
    examples:
    - value: H3BO3;6.2 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium micronutrients
    rank: 276
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000579
    alias: root_med_micronutr
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  root_med_ph:
    name: root_med_ph
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      occurrence:
        tag: occurrence
        value: '1'
    description: pH measurement of the culture rooting medium; e.g. 5.5.
    title: rooting medium pH
    examples:
    - value: '7.5'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium pH
    rank: 277
    is_a: core field
    slot_uri: MIXS:0001062
    alias: root_med_ph
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  root_med_regl:
    name: root_med_regl
    annotations:
      expected_value:
        tag: expected_value
        value: regulator name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Growth regulators in the culture rooting medium such as cytokinins,
      auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA.
    title: rooting medium regulators
    examples:
    - value: abscisic acid;0.75 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium regulators
    rank: 278
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000581
    alias: root_med_regl
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  root_med_solid:
    name: root_med_solid
    annotations:
      expected_value:
        tag: expected_value
        value: name
      occurrence:
        tag: occurrence
        value: '1'
    description: Specification of the solidifying agent in the culture rooting medium;
      e.g. agar.
    title: rooting medium solidifier
    examples:
    - value: agar
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium solidifier
    rank: 279
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001063
    alias: root_med_solid
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  root_med_suppl:
    name: root_med_suppl
    annotations:
      expected_value:
        tag: expected_value
        value: supplement name;measurement value
      preferred_unit:
        tag: preferred_unit
        value: milligram per liter
      occurrence:
        tag: occurrence
        value: '1'
    description: Organic supplements of the culture rooting medium, such as vitamins,
      amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid
      (0.5 mg/L).
    title: rooting medium organic supplements
    examples:
    - value: nicotinic acid;0.5 milligram per liter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - rooting medium organic supplements
    rank: 280
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000580
    alias: root_med_suppl
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
    pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
  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: PlantAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  salinity_meth:
    name: salinity_meth
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI or url
      occurrence:
        tag: occurrence
        value: '1'
    description: Reference or method used in determining salinity
    title: salinity method
    examples:
    - value: https://doi.org/10.1007/978-1-61779-986-0_28
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - salinity method
    rank: 55
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000341
    alias: salinity_meth
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    multivalued: false
  salt_regm:
    name: salt_regm
    annotations:
      expected_value:
        tag: expected_value
        value: salt name;salt amount;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: gram, microgram, mole per liter, gram per liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving use of salts as supplement
      to liquid and soil growth media; should include the name of salt, amount administered,
      treatment regimen including how many times the treatment was repeated, how long
      each treatment lasted, and the start and end time of the entire treatment; can
      include multiple salt regimens
    title: salt regimen
    examples:
    - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - salt regimen
    rank: 281
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000582
    alias: salt_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  samp_capt_status:
    name: samp_capt_status
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Reason for the sample
    title: sample capture status
    examples:
    - value: farm sample
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample capture status
    rank: 282
    is_a: core field
    slot_uri: MIXS:0000860
    alias: samp_capt_status
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: samp_capt_status_enum
    multivalued: false
  samp_collec_device:
    name: samp_collec_device
    annotations:
      expected_value:
        tag: expected_value
        value: device name
    description: The device used to collect an environmental sample. This field accepts
      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
    title: sample collection device
    comments:
    - Report dimensions and details when applicable
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample collection device
    rank: 14
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000002
    alias: samp_collec_device
    owner: PlantAssociatedInterface
    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: PlantAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    multivalued: false
  samp_dis_stage:
    name: samp_dis_stage
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Stage of the disease at the time of sample collection, e.g. inoculation,
      penetration, infection, growth and reproduction, dissemination of pathogen.
    title: sample disease stage
    examples:
    - value: infection
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample disease stage
    rank: 283
    is_a: core field
    slot_uri: MIXS:0000249
    alias: samp_dis_stage
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: samp_dis_stage_enum
    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: PlantAssociatedInterface
    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: PlantAssociatedInterface
    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: PlantAssociatedInterface
    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: PlantAssociatedInterface
    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: PlantAssociatedInterface
    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: PlantAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    - SampIdNewTermsMixin
    slot_group: sample_id_section
    range: string
    recommended: true
    multivalued: false
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'
  season_environment:
    name: season_environment
    annotations:
      expected_value:
        tag: expected_value
        value: seasonal environment name;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Treatment involving an exposure to a particular season (e.g. Winter,
      summer, rabi, rainy etc.), treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment
    title: seasonal environment
    examples:
    - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - seasonal environment
    rank: 284
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001068
    alias: season_environment
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    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: PlantAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  specific_ecosystem:
    name: specific_ecosystem
    description: Specific ecosystems represent specific features of the environment
      like aphotic zone in an ocean or gastric mucosa within a host digestive system.
      Specific ecosystem is in position 5/5 in a GOLD path.
    comments:
    - Specific ecosystems help to define samples based on very specific characteristics
      of an environment under the five-level classification system.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://gold.jgi.doe.gov/help
    rank: 13
    is_a: gold_path_field
    alias: specific_ecosystem
    owner: PlantAssociatedInterface
    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
  standing_water_regm:
    name: standing_water_regm
    annotations:
      expected_value:
        tag: expected_value
        value: standing water type;treatment interval and duration
      occurrence:
        tag: occurrence
        value: m
    description: Treatment involving an exposure to standing water during a plant's
      life span, types can be flood water or standing water, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple regimens
    title: standing water regimen
    examples:
    - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - standing water regimen
    rank: 286
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001069
    alias: standing_water_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  start_date_inc:
    name: start_date_inc
    description: Date the incubation was started. Only relevant for incubation samples.
    title: incubation start date
    notes:
    - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
      date only
    comments:
    - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
      are all acceptable.
    examples:
    - value: 2021-04-15, 2021-04 and 2021 are all acceptable.
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIXS:0000011
    rank: 4
    string_serialization: '{date, arbitrary precision}'
    alias: start_date_inc
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    - SoilMixsInspiredMixin
    slot_group: mixs_inspired_section
    range: string
    recommended: true
    multivalued: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  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: PlantAssociatedInterface
    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.*$
  tiss_cult_growth_med:
    name: tiss_cult_growth_med
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url or free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Description of plant tissue culture growth media used
    title: tissue culture growth media
    examples:
    - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - tissue culture growth media
    rank: 287
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001070
    alias: tiss_cult_growth_med
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  water_temp_regm:
    name: water_temp_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to water with varying
      degree of temperature, treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment; can include multiple regimens
    title: water temperature regimen
    examples:
    - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - water temperature regimen
    rank: 288
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000590
    alias: water_temp_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    multivalued: false
  watering_regm:
    name: watering_regm
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value;treatment interval and duration
      preferred_unit:
        tag: preferred_unit
        value: milliliter, liter
      occurrence:
        tag: occurrence
        value: m
    description: Information about treatment involving an exposure to watering frequencies,
      treatment regimen including how many times the treatment was repeated, how long
      each treatment lasted, and the start and end time of the entire treatment; can
      include multiple regimens
    title: watering regimen
    examples:
    - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    - value: 75% water holding capacity; constant
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - watering regimen
    rank: 25
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000591
    alias: watering_regm
    owner: PlantAssociatedInterface
    domain_of:
    - Biosample
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    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: PlantAssociatedInterface
    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: PlantAssociatedInterface
    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: PlantAssociatedInterface
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    multivalued: false
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'