Class: Host Associated (HostAssociatedInterface)

host_associated dh_interface

URI: nmdc_sub_schema:HostAssociatedInterface

classDiagram class HostAssociatedInterface DhMultiviewCommonColumnsMixin <|-- HostAssociatedInterface SampIdNewTermsMixin <|-- HostAssociatedInterface DhInterface <|-- HostAssociatedInterface HostAssociatedInterface : alt HostAssociatedInterface : analysis_type HostAssociatedInterface --|> AnalysisTypeEnum : analysis_type HostAssociatedInterface : ances_data HostAssociatedInterface : biol_stat HostAssociatedInterface --|> biol_stat_enum : biol_stat HostAssociatedInterface : blood_press_diast HostAssociatedInterface : blood_press_syst HostAssociatedInterface : chem_administration HostAssociatedInterface : collection_date HostAssociatedInterface : depth HostAssociatedInterface : ecosystem HostAssociatedInterface --|> EcosystemEnum : ecosystem HostAssociatedInterface : ecosystem_category HostAssociatedInterface --|> EcosystemCategoryEnum : ecosystem_category HostAssociatedInterface : ecosystem_subtype HostAssociatedInterface --|> EcosystemSubtypeEnum : ecosystem_subtype HostAssociatedInterface : ecosystem_type HostAssociatedInterface --|> EcosystemTypeEnum : ecosystem_type HostAssociatedInterface : elev HostAssociatedInterface : env_broad_scale HostAssociatedInterface : env_local_scale HostAssociatedInterface : env_medium HostAssociatedInterface : experimental_factor HostAssociatedInterface : genetic_mod HostAssociatedInterface : geo_loc_name HostAssociatedInterface : gravidity HostAssociatedInterface : host_age HostAssociatedInterface : host_body_habitat HostAssociatedInterface : host_body_product HostAssociatedInterface : host_body_site HostAssociatedInterface : host_body_temp HostAssociatedInterface : host_color HostAssociatedInterface : host_common_name HostAssociatedInterface : host_diet HostAssociatedInterface : host_disease_stat HostAssociatedInterface : host_dry_mass HostAssociatedInterface : host_family_relation HostAssociatedInterface : host_genotype HostAssociatedInterface : host_growth_cond HostAssociatedInterface : host_height HostAssociatedInterface : host_last_meal HostAssociatedInterface : host_length HostAssociatedInterface : host_life_stage HostAssociatedInterface : host_phenotype HostAssociatedInterface : host_sex HostAssociatedInterface --|> host_sex_enum : host_sex HostAssociatedInterface : host_shape HostAssociatedInterface : host_subject_id HostAssociatedInterface : host_subspecf_genlin HostAssociatedInterface : host_substrate HostAssociatedInterface : host_symbiont HostAssociatedInterface : host_taxid HostAssociatedInterface : host_tot_mass HostAssociatedInterface : lat_lon HostAssociatedInterface : misc_param HostAssociatedInterface : organism_count HostAssociatedInterface : oxy_stat_samp HostAssociatedInterface --|> OxyStatSampEnum : oxy_stat_samp HostAssociatedInterface : perturbation HostAssociatedInterface : salinity HostAssociatedInterface : samp_capt_status HostAssociatedInterface --|> samp_capt_status_enum : samp_capt_status HostAssociatedInterface : samp_collec_device HostAssociatedInterface : samp_collec_method HostAssociatedInterface : samp_dis_stage HostAssociatedInterface --|> samp_dis_stage_enum : samp_dis_stage HostAssociatedInterface : samp_mat_process HostAssociatedInterface : samp_name HostAssociatedInterface : samp_size HostAssociatedInterface : samp_store_dur HostAssociatedInterface : samp_store_loc HostAssociatedInterface : samp_store_temp HostAssociatedInterface : sample_link HostAssociatedInterface : size_frac HostAssociatedInterface : source_mat_id HostAssociatedInterface : specific_ecosystem HostAssociatedInterface --|> SpecificEcosystemEnum : specific_ecosystem HostAssociatedInterface : temp

Inheritance

DhInterface
- HostAssociatedInterface [ DhMultiviewCommonColumnsMixin SampIdNewTermsMixin]

Slots

Name	Cardinality and Range	Description	Inheritance
alt	0..1 recommended String	Altitude is a term used to identify heights of objects such as airplanes, spa...	direct
ances_data	0..1 String	Information about either pedigree or other ancestral information description ...	direct
biol_stat	0..1 BiolStatEnum	The level of genome modification	direct
blood_press_diast	0..1 String	Resting diastolic blood pressure, measured as mm mercury	direct
blood_press_syst	0..1 String	Resting systolic blood pressure, measured as mm mercury	direct
chem_administration	0..1 recommended String	List of chemical compounds administered to the host or site where sampling oc...	direct
collection_date	1..1 String	The date of sampling	direct
depth	0..1 recommended String	The vertical distance below local surface, e	direct
ecosystem	0..1 recommended EcosystemEnum	An ecosystem is a combination of a physical environment (abiotic factors) and...	direct
ecosystem_category	0..1 recommended EcosystemCategoryEnum	Ecosystem categories represent divisions within the ecosystem based on specif...	direct
ecosystem_subtype	0..1 recommended EcosystemSubtypeEnum	Ecosystem subtypes represent further subdivision of Ecosystem types into more...	direct
ecosystem_type	0..1 recommended EcosystemTypeEnum	Ecosystem types represent things having common characteristics within the Eco...	direct
elev	1..1 Float	Elevation of the sampling site is its height above a fixed reference point, m...	direct
env_broad_scale	1..1 String	In this field, report which major environmental system your sample or specime...	direct
env_local_scale	1..1 String	Report the entity or entities which are in the sample or specimen’s local vic...	direct
env_medium	1..1 String	Report the environmental material(s) immediately surrounding the sample or sp...	direct
experimental_factor	0..1 String	Experimental factors are essentially the variable aspects of an experiment de...	direct
genetic_mod	0..1 String	Genetic modifications of the genome of an organism, which may occur naturally...	direct
geo_loc_name	1..1 String	The geographical origin of the sample as defined by the country or sea name f...	direct
gravidity	0..1 String	Whether or not subject is gravid, and if yes date due or date post-conception...	direct
host_age	0..1 String	Age of host at the time of sampling; relevant scale depends on species and st...	direct
host_body_habitat	0..1 String	Original body habitat where the sample was obtained from	direct
host_body_product	0..1 String	Substance produced by the body, e	direct
host_body_site	0..1 String	Name of body site where the sample was obtained from, such as a specific orga...	direct
host_body_temp	0..1 String	Core body temperature of the host when sample was collected	direct
host_color	0..1 String	The color of host	direct
host_common_name	0..1 String	Common name of the host	direct
host_diet	0..1 String	Type of diet depending on the host, for animals omnivore, herbivore etc	direct
host_disease_stat	0..1 String	List of diseases with which the host has been diagnosed; can include multiple...	direct
host_dry_mass	0..1 String	Measurement of dry mass	direct
host_family_relation	0..1 String	Familial relationships to other hosts in the same study; can include multiple...	direct
host_genotype	0..1 String	Observed genotype	direct
host_growth_cond	0..1 String	Literature reference giving growth conditions of the host	direct
host_height	0..1 String	The height of subject	direct
host_last_meal	0..1 String	Content of last meal and time since feeding; can include multiple values	direct
host_length	0..1 String	The length of subject	direct
host_life_stage	0..1 String	Description of life stage of host	direct
host_phenotype	0..1 String	Phenotype of human or other host	direct
host_sex	0..1 HostSexEnum	Gender or physical sex of the host	direct
host_shape	0..1 String	Morphological shape of host	direct
host_subject_id	0..1 String	A unique identifier by which each subject can be referred to, de-identified	direct
host_subspecf_genlin	0..1 String	Information about the genetic distinctness of the host organism below the sub...	direct
host_substrate	0..1 String	The growth substrate of the host	direct
host_symbiont	0..1 String	The taxonomic name of the organism(s) found living in mutualistic, commensali...	direct
host_taxid	0..1 String	NCBI taxon id of the host, e	direct
host_tot_mass	0..1 String	Total mass of the host at collection, the unit depends on host	direct
lat_lon	1..1 String	The geographical origin of the sample as defined by latitude and longitude	direct
misc_param	0..1 String	Any other measurement performed or parameter collected, that is not listed he...	direct
organism_count	0..1 String	Total cell count of any organism (or group of organisms) per gram, volume or ...	direct
oxy_stat_samp	0..1 OxyStatSampEnum	Oxygenation status of sample	direct
perturbation	0..1 String	Type of perturbation, e	direct
salinity	0..1 String	The total concentration of all dissolved salts in a liquid or solid sample	direct
samp_capt_status	0..1 SampCaptStatusEnum	Reason for the sample	direct
samp_collec_device	0..1 recommended String	The device used to collect an environmental sample	direct
samp_collec_method	0..1 String	The method employed for collecting the sample	direct
samp_dis_stage	0..1 SampDisStageEnum	Stage of the disease at the time of sample collection, e	direct
samp_mat_process	0..1 String	A brief description of any processing applied to the sample during or after r...	direct
samp_size	0..1 String	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...	direct
samp_store_dur	0..1 String	Duration for which the sample was stored	direct
samp_store_loc	0..1 String	Location at which sample was stored, usually name of a specific freezer/room	direct
samp_store_temp	1..1 String	Temperature at which the sample was stored (degrees are assumed)	direct
sample_link	0..1 recommended String	A unique identifier to assign parent-child, subsample, or sibling samples	direct
size_frac	0..1 String	Filtering pore size used in sample preparation	direct
specific_ecosystem	0..1 recommended SpecificEcosystemEnum	Specific ecosystems represent specific features of the environment like aphot...	direct
temp	0..1 String	Temperature of the sample at the time of sampling	direct
analysis_type	1..* AnalysisTypeEnum	Select all the data types associated or available for this biosample	DhMultiviewCommonColumnsMixin
samp_name	1..1 String	A local identifier or name that for the material sample collected	DhMultiviewCommonColumnsMixin
source_mat_id	0..1 String	A globally unique identifier assigned to the biological sample	DhMultiviewCommonColumnsMixin

Usages

used by	used in	type	used
SampleData	host_associated_data	range	HostAssociatedInterface

Identifier and Mapping Information

Annotations

property	value
excel_worksheet_name	host-associated

Schema Source

from schema: https://example.com/nmdc_submission_schema

Mappings

Mapping Type	Mapped Value
self	nmdc_sub_schema:HostAssociatedInterface
native	nmdc_sub_schema:HostAssociatedInterface

LinkML Source

Direct

name: HostAssociatedInterface
annotations:
  excel_worksheet_name:
    tag: excel_worksheet_name
    value: host-associated
description: host_associated dh_interface
title: Host Associated
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
- SampIdNewTermsMixin
slots:
- alt
- ances_data
- biol_stat
- blood_press_diast
- blood_press_syst
- chem_administration
- collection_date
- depth
- ecosystem
- ecosystem_category
- ecosystem_subtype
- ecosystem_type
- elev
- env_broad_scale
- env_local_scale
- env_medium
- experimental_factor
- genetic_mod
- geo_loc_name
- gravidity
- host_age
- host_body_habitat
- host_body_product
- host_body_site
- host_body_temp
- host_color
- host_common_name
- host_diet
- host_disease_stat
- host_dry_mass
- host_family_relation
- host_genotype
- host_growth_cond
- host_height
- host_last_meal
- host_length
- host_life_stage
- host_phenotype
- host_sex
- host_shape
- host_subject_id
- host_subspecf_genlin
- host_substrate
- host_symbiont
- host_taxid
- host_tot_mass
- lat_lon
- misc_param
- organism_count
- oxy_stat_samp
- perturbation
- salinity
- 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
- size_frac
- specific_ecosystem
- temp
slot_usage:
  alt:
    name: alt
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: Altitude is a term used to identify heights of objects such as airplanes,
      space shuttles, rockets, atmospheric balloons and heights of places such as
      atmospheric layers and clouds. It is used to measure the height of an object
      which is above the earth's surface. In this context, the altitude measurement
      is the vertical distance between the earth's surface above sea level and the
      sampled position in the air
    title: altitude
    examples:
    - value: 100 meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - altitude
    rank: 26
    is_a: environment field
    slot_uri: MIXS:0000094
    multivalued: false
    owner: Biosample
    domain_of:
    - agriculture
    - air
    - built environment
    - core
    - food-animal and animal feed
    - food-farm environment
    - food-food production facility
    - food-human foods
    - host-associated
    - human-associated
    - human-gut
    - human-oral
    - human-skin
    - human-vaginal
    - hydrocarbon resources-cores
    - hydrocarbon resources-fluids_swabs
    - microbial mat_biofilm
    - miscellaneous natural or artificial environment
    - plant-associated
    - sediment
    - soil
    - symbiont-associated
    - wastewater_sludge
    - water
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: biol_stat_enum
  blood_press_diast:
    name: blood_press_diast
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millimeter mercury
      occurrence:
        tag: occurrence
        value: '1'
    description: Resting diastolic blood pressure, measured as mm mercury
    title: host blood pressure diastolic
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host blood pressure diastolic
    rank: 299
    is_a: core field
    slot_uri: MIXS:0000258
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  blood_press_syst:
    name: blood_press_syst
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millimeter mercury
      occurrence:
        tag: occurrence
        value: '1'
    description: Resting systolic blood pressure, measured as mm mercury
    title: host blood pressure systolic
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host blood pressure systolic
    rank: 300
    is_a: core field
    slot_uri: MIXS:0000259
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  chem_administration:
    name: chem_administration
    annotations:
      expected_value:
        tag: expected_value
        value: CHEBI;timestamp
      occurrence:
        tag: occurrence
        value: m
    description: List of chemical compounds administered to the host or site where
      sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
      include multiple compounds. For chemical entities of biological interest ontology
      (chebi) (v 163), http://purl.bioontology.org/ontology/chebi
    title: chemical administration
    examples:
    - value: agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22
    - value: agar [CHEBI:2509];2018-05
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chemical administration
    rank: 17
    is_a: core field
    string_serialization: '{termLabel} {[termID]};{timestamp}'
    slot_uri: MIXS:0000751
    multivalued: false
    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
    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)?)?)?)?$
  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
    multivalued: false
    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
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  depth:
    name: depth
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: The vertical distance below local surface, e.g. for sediment or soil
      samples depth is measured from sediment or soil surface, respectively. Depth
      can be reported as an interval for subsurface samples.
    title: depth, meters
    notes:
    - Use modified term
    comments:
    - All depths must be reported in meters. Provide the numerical portion only.
    examples:
    - value: 0 - 0.1
    - value: '1'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - depth
    rank: 9
    is_a: environment field
    string_serialization: '{float}|{float}-{float}'
    slot_uri: MIXS:0000018
    multivalued: false
    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
    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
    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
    rank: 6
    is_a: environment field
    slot_uri: MIXS:0000093
    multivalued: false
    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
  env_broad_scale:
    name: env_broad_scale
    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)
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 6
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    multivalued: false
    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
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  env_local_scale:
    name: env_local_scale
    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
    rank: 7
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000013
    multivalued: false
    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
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  env_medium:
    name: env_medium
    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
    rank: 8
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000014
    multivalued: false
    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
    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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    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
    pattern: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  gravidity:
    name: gravidity
    annotations:
      expected_value:
        tag: expected_value
        value: gravidity status;timestamp
      occurrence:
        tag: occurrence
        value: '1'
    description: Whether or not subject is gravid, and if yes date due or date post-conception,
      specifying which is used
    title: gravidity
    examples:
    - value: yes;due date:2018-05-11
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gravidity
    rank: 312
    is_a: core field
    string_serialization: '{boolean};{timestamp}'
    slot_uri: MIXS:0000875
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_age:
    name: host_age
    annotations:
      expected_value:
        tag: expected_value
        value: value
      preferred_unit:
        tag: preferred_unit
        value: year, day, hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Age of host at the time of sampling; relevant scale depends on species
      and study, e.g. Could be seconds for amoebae or centuries for trees
    title: host age
    examples:
    - value: 10 days
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host age
    rank: 249
    is_a: core field
    slot_uri: MIXS:0000255
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_body_habitat:
    name: host_body_habitat
    annotations:
      expected_value:
        tag: expected_value
        value: free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Original body habitat where the sample was obtained from
    title: host body habitat
    examples:
    - value: nasopharynx
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host body habitat
    rank: 319
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000866
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_body_product:
    name: host_body_product
    annotations:
      expected_value:
        tag: expected_value
        value: FMA or UBERON
      occurrence:
        tag: occurrence
        value: '1'
    description: Substance produced by the body, e.g. Stool, mucus, where the sample
      was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy
      ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma
      or https://www.ebi.ac.uk/ols/ontologies/uberon
    title: host body product
    examples:
    - value: Portion of mucus [fma66938]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host body product
    rank: 320
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000888
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  host_body_site:
    name: host_body_site
    annotations:
      expected_value:
        tag: expected_value
        value: FMA or UBERON
      occurrence:
        tag: occurrence
        value: '1'
    description: Name of body site where the sample was obtained from, such as a specific
      organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology
      (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,
      please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON
    title: host body site
    examples:
    - value: gill [UBERON:0002535]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host body site
    rank: 321
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000867
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  host_body_temp:
    name: host_body_temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: '1'
    description: Core body temperature of the host when sample was collected
    title: host body temperature
    examples:
    - value: 15 degree Celsius
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host body temperature
    rank: 322
    is_a: core field
    slot_uri: MIXS:0000274
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_color:
    name: host_color
    annotations:
      expected_value:
        tag: expected_value
        value: color
      occurrence:
        tag: occurrence
        value: '1'
    description: The color of host
    title: host color
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host color
    rank: 323
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000260
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_diet:
    name: host_diet
    annotations:
      expected_value:
        tag: expected_value
        value: diet type
      occurrence:
        tag: occurrence
        value: m
    description: Type of diet depending on the host, for animals omnivore, herbivore
      etc., for humans high-fat, meditteranean etc.; can include multiple diet types
    title: host diet
    examples:
    - value: herbivore
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host diet
    rank: 324
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000869
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_family_relation:
    name: host_family_relation
    annotations:
      expected_value:
        tag: expected_value
        value: relationship type;arbitrary identifier
      occurrence:
        tag: occurrence
        value: m
    description: Familial relationships to other hosts in the same study; can include
      multiple relationships
    title: host family relationship
    examples:
    - value: offspring;Mussel25
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host family relationship
    rank: 325
    is_a: core field
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0000872
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_growth_cond:
    name: host_growth_cond
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url or free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Literature reference giving growth conditions of the host
    title: host growth conditions
    examples:
    - value: https://academic.oup.com/icesjms/article/68/2/349/617247
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host growth conditions
    rank: 326
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0000871
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_last_meal:
    name: host_last_meal
    annotations:
      expected_value:
        tag: expected_value
        value: content;duration
      occurrence:
        tag: occurrence
        value: m
    description: Content of last meal and time since feeding; can include multiple
      values
    title: host last meal
    examples:
    - value: corn feed;P2H
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host last meal
    rank: 327
    is_a: core field
    string_serialization: '{text};{duration}'
    slot_uri: MIXS:0000870
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  host_sex:
    name: host_sex
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Gender or physical sex of the host.
    title: host sex
    examples:
    - value: non-binary
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host sex
    rank: 328
    is_a: core field
    slot_uri: MIXS:0000811
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: host_sex_enum
  host_shape:
    name: host_shape
    annotations:
      expected_value:
        tag: expected_value
        value: shape
      occurrence:
        tag: occurrence
        value: '1'
    description: Morphological shape of host
    title: host shape
    examples:
    - value: round
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host shape
    rank: 329
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000261
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_subject_id:
    name: host_subject_id
    annotations:
      expected_value:
        tag: expected_value
        value: unique identifier
      occurrence:
        tag: occurrence
        value: '1'
    description: A unique identifier by which each subject can be referred to, de-identified.
    title: host subject id
    examples:
    - value: MPI123
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host subject id
    rank: 330
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000861
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_substrate:
    name: host_substrate
    annotations:
      expected_value:
        tag: expected_value
        value: substrate name
      occurrence:
        tag: occurrence
        value: '1'
    description: The growth substrate of the host.
    title: host substrate
    examples:
    - value: rock
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host substrate
    rank: 331
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000252
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  lat_lon:
    name: lat_lon
    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
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 5
    is_a: environment field
    string_serialization: '{lat lon}'
    slot_uri: MIXS:0000009
    multivalued: false
    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
    pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      [^;\t\r\x0A]+)$
  organism_count:
    name: organism_count
    annotations:
      expected_value:
        tag: expected_value
        value: organism name;measurement value;enumeration
      preferred_unit:
        tag: preferred_unit
        value: number of cells per cubic meter, number of cells per milliliter, number
          of cells per cubic centimeter
      occurrence:
        tag: occurrence
        value: m
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organism count
    rank: 30
    is_a: core field
    slot_uri: MIXS:0000103
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: OxyStatSampEnum
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: samp_capt_status_enum
  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
    multivalued: false
    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
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: samp_dis_stage_enum
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    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
    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}'
    multivalued: false
    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
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
  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
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  horizon_meth:
    name: horizon_meth
    title: horizon method

Induced

name: HostAssociatedInterface
annotations:
  excel_worksheet_name:
    tag: excel_worksheet_name
    value: host-associated
description: host_associated dh_interface
title: Host Associated
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
- SampIdNewTermsMixin
slot_usage:
  alt:
    name: alt
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: Altitude is a term used to identify heights of objects such as airplanes,
      space shuttles, rockets, atmospheric balloons and heights of places such as
      atmospheric layers and clouds. It is used to measure the height of an object
      which is above the earth's surface. In this context, the altitude measurement
      is the vertical distance between the earth's surface above sea level and the
      sampled position in the air
    title: altitude
    examples:
    - value: 100 meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - altitude
    rank: 26
    is_a: environment field
    slot_uri: MIXS:0000094
    multivalued: false
    owner: Biosample
    domain_of:
    - agriculture
    - air
    - built environment
    - core
    - food-animal and animal feed
    - food-farm environment
    - food-food production facility
    - food-human foods
    - host-associated
    - human-associated
    - human-gut
    - human-oral
    - human-skin
    - human-vaginal
    - hydrocarbon resources-cores
    - hydrocarbon resources-fluids_swabs
    - microbial mat_biofilm
    - miscellaneous natural or artificial environment
    - plant-associated
    - sediment
    - soil
    - symbiont-associated
    - wastewater_sludge
    - water
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: biol_stat_enum
  blood_press_diast:
    name: blood_press_diast
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millimeter mercury
      occurrence:
        tag: occurrence
        value: '1'
    description: Resting diastolic blood pressure, measured as mm mercury
    title: host blood pressure diastolic
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host blood pressure diastolic
    rank: 299
    is_a: core field
    slot_uri: MIXS:0000258
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  blood_press_syst:
    name: blood_press_syst
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millimeter mercury
      occurrence:
        tag: occurrence
        value: '1'
    description: Resting systolic blood pressure, measured as mm mercury
    title: host blood pressure systolic
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host blood pressure systolic
    rank: 300
    is_a: core field
    slot_uri: MIXS:0000259
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  chem_administration:
    name: chem_administration
    annotations:
      expected_value:
        tag: expected_value
        value: CHEBI;timestamp
      occurrence:
        tag: occurrence
        value: m
    description: List of chemical compounds administered to the host or site where
      sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
      include multiple compounds. For chemical entities of biological interest ontology
      (chebi) (v 163), http://purl.bioontology.org/ontology/chebi
    title: chemical administration
    examples:
    - value: agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22
    - value: agar [CHEBI:2509];2018-05
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chemical administration
    rank: 17
    is_a: core field
    string_serialization: '{termLabel} {[termID]};{timestamp}'
    slot_uri: MIXS:0000751
    multivalued: false
    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
    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)?)?)?)?$
  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
    multivalued: false
    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
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  depth:
    name: depth
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: The vertical distance below local surface, e.g. for sediment or soil
      samples depth is measured from sediment or soil surface, respectively. Depth
      can be reported as an interval for subsurface samples.
    title: depth, meters
    notes:
    - Use modified term
    comments:
    - All depths must be reported in meters. Provide the numerical portion only.
    examples:
    - value: 0 - 0.1
    - value: '1'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - depth
    rank: 9
    is_a: environment field
    string_serialization: '{float}|{float}-{float}'
    slot_uri: MIXS:0000018
    multivalued: false
    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
    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
    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
    rank: 6
    is_a: environment field
    slot_uri: MIXS:0000093
    multivalued: false
    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
  env_broad_scale:
    name: env_broad_scale
    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)
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 6
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    multivalued: false
    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
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  env_local_scale:
    name: env_local_scale
    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
    rank: 7
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000013
    multivalued: false
    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
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  env_medium:
    name: env_medium
    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
    rank: 8
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000014
    multivalued: false
    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
    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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    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
    pattern: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  gravidity:
    name: gravidity
    annotations:
      expected_value:
        tag: expected_value
        value: gravidity status;timestamp
      occurrence:
        tag: occurrence
        value: '1'
    description: Whether or not subject is gravid, and if yes date due or date post-conception,
      specifying which is used
    title: gravidity
    examples:
    - value: yes;due date:2018-05-11
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gravidity
    rank: 312
    is_a: core field
    string_serialization: '{boolean};{timestamp}'
    slot_uri: MIXS:0000875
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_age:
    name: host_age
    annotations:
      expected_value:
        tag: expected_value
        value: value
      preferred_unit:
        tag: preferred_unit
        value: year, day, hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Age of host at the time of sampling; relevant scale depends on species
      and study, e.g. Could be seconds for amoebae or centuries for trees
    title: host age
    examples:
    - value: 10 days
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host age
    rank: 249
    is_a: core field
    slot_uri: MIXS:0000255
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_body_habitat:
    name: host_body_habitat
    annotations:
      expected_value:
        tag: expected_value
        value: free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Original body habitat where the sample was obtained from
    title: host body habitat
    examples:
    - value: nasopharynx
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host body habitat
    rank: 319
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000866
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_body_product:
    name: host_body_product
    annotations:
      expected_value:
        tag: expected_value
        value: FMA or UBERON
      occurrence:
        tag: occurrence
        value: '1'
    description: Substance produced by the body, e.g. Stool, mucus, where the sample
      was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy
      ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma
      or https://www.ebi.ac.uk/ols/ontologies/uberon
    title: host body product
    examples:
    - value: Portion of mucus [fma66938]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host body product
    rank: 320
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000888
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  host_body_site:
    name: host_body_site
    annotations:
      expected_value:
        tag: expected_value
        value: FMA or UBERON
      occurrence:
        tag: occurrence
        value: '1'
    description: Name of body site where the sample was obtained from, such as a specific
      organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology
      (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,
      please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON
    title: host body site
    examples:
    - value: gill [UBERON:0002535]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host body site
    rank: 321
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000867
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  host_body_temp:
    name: host_body_temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: '1'
    description: Core body temperature of the host when sample was collected
    title: host body temperature
    examples:
    - value: 15 degree Celsius
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host body temperature
    rank: 322
    is_a: core field
    slot_uri: MIXS:0000274
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_color:
    name: host_color
    annotations:
      expected_value:
        tag: expected_value
        value: color
      occurrence:
        tag: occurrence
        value: '1'
    description: The color of host
    title: host color
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host color
    rank: 323
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000260
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_diet:
    name: host_diet
    annotations:
      expected_value:
        tag: expected_value
        value: diet type
      occurrence:
        tag: occurrence
        value: m
    description: Type of diet depending on the host, for animals omnivore, herbivore
      etc., for humans high-fat, meditteranean etc.; can include multiple diet types
    title: host diet
    examples:
    - value: herbivore
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host diet
    rank: 324
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000869
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_family_relation:
    name: host_family_relation
    annotations:
      expected_value:
        tag: expected_value
        value: relationship type;arbitrary identifier
      occurrence:
        tag: occurrence
        value: m
    description: Familial relationships to other hosts in the same study; can include
      multiple relationships
    title: host family relationship
    examples:
    - value: offspring;Mussel25
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host family relationship
    rank: 325
    is_a: core field
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0000872
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_growth_cond:
    name: host_growth_cond
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url or free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Literature reference giving growth conditions of the host
    title: host growth conditions
    examples:
    - value: https://academic.oup.com/icesjms/article/68/2/349/617247
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host growth conditions
    rank: 326
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0000871
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_last_meal:
    name: host_last_meal
    annotations:
      expected_value:
        tag: expected_value
        value: content;duration
      occurrence:
        tag: occurrence
        value: m
    description: Content of last meal and time since feeding; can include multiple
      values
    title: host last meal
    examples:
    - value: corn feed;P2H
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host last meal
    rank: 327
    is_a: core field
    string_serialization: '{text};{duration}'
    slot_uri: MIXS:0000870
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  host_sex:
    name: host_sex
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Gender or physical sex of the host.
    title: host sex
    examples:
    - value: non-binary
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host sex
    rank: 328
    is_a: core field
    slot_uri: MIXS:0000811
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: host_sex_enum
  host_shape:
    name: host_shape
    annotations:
      expected_value:
        tag: expected_value
        value: shape
      occurrence:
        tag: occurrence
        value: '1'
    description: Morphological shape of host
    title: host shape
    examples:
    - value: round
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host shape
    rank: 329
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000261
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_subject_id:
    name: host_subject_id
    annotations:
      expected_value:
        tag: expected_value
        value: unique identifier
      occurrence:
        tag: occurrence
        value: '1'
    description: A unique identifier by which each subject can be referred to, de-identified.
    title: host subject id
    examples:
    - value: MPI123
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host subject id
    rank: 330
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000861
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_substrate:
    name: host_substrate
    annotations:
      expected_value:
        tag: expected_value
        value: substrate name
      occurrence:
        tag: occurrence
        value: '1'
    description: The growth substrate of the host.
    title: host substrate
    examples:
    - value: rock
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host substrate
    rank: 331
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000252
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  lat_lon:
    name: lat_lon
    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
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 5
    is_a: environment field
    string_serialization: '{lat lon}'
    slot_uri: MIXS:0000009
    multivalued: false
    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
    pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      [^;\t\r\x0A]+)$
  organism_count:
    name: organism_count
    annotations:
      expected_value:
        tag: expected_value
        value: organism name;measurement value;enumeration
      preferred_unit:
        tag: preferred_unit
        value: number of cells per cubic meter, number of cells per milliliter, number
          of cells per cubic centimeter
      occurrence:
        tag: occurrence
        value: m
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organism count
    rank: 30
    is_a: core field
    slot_uri: MIXS:0000103
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: OxyStatSampEnum
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: samp_capt_status_enum
  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
    multivalued: false
    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
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: samp_dis_stage_enum
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    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
    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}'
    multivalued: false
    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
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
  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
  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
    multivalued: false
    owner: Biosample
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  horizon_meth:
    name: horizon_meth
    title: horizon method
attributes:
  alt:
    name: alt
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: Altitude is a term used to identify heights of objects such as airplanes,
      space shuttles, rockets, atmospheric balloons and heights of places such as
      atmospheric layers and clouds. It is used to measure the height of an object
      which is above the earth's surface. In this context, the altitude measurement
      is the vertical distance between the earth's surface above sea level and the
      sampled position in the air
    title: altitude
    examples:
    - value: 100 meter
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - altitude
    rank: 26
    is_a: environment field
    slot_uri: MIXS:0000094
    multivalued: false
    alias: alt
    owner: HostAssociatedInterface
    domain_of:
    - agriculture
    - air
    - built environment
    - core
    - food-animal and animal feed
    - food-farm environment
    - food-food production facility
    - food-human foods
    - host-associated
    - human-associated
    - human-gut
    - human-oral
    - human-skin
    - human-vaginal
    - hydrocarbon resources-cores
    - hydrocarbon resources-fluids_swabs
    - microbial mat_biofilm
    - miscellaneous natural or artificial environment
    - plant-associated
    - sediment
    - soil
    - symbiont-associated
    - wastewater_sludge
    - water
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
    multivalued: false
    alias: ances_data
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: biol_stat
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: biol_stat_enum
  blood_press_diast:
    name: blood_press_diast
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millimeter mercury
      occurrence:
        tag: occurrence
        value: '1'
    description: Resting diastolic blood pressure, measured as mm mercury
    title: host blood pressure diastolic
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host blood pressure diastolic
    rank: 299
    is_a: core field
    slot_uri: MIXS:0000258
    multivalued: false
    alias: blood_press_diast
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  blood_press_syst:
    name: blood_press_syst
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: millimeter mercury
      occurrence:
        tag: occurrence
        value: '1'
    description: Resting systolic blood pressure, measured as mm mercury
    title: host blood pressure systolic
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host blood pressure systolic
    rank: 300
    is_a: core field
    slot_uri: MIXS:0000259
    multivalued: false
    alias: blood_press_syst
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  chem_administration:
    name: chem_administration
    annotations:
      expected_value:
        tag: expected_value
        value: CHEBI;timestamp
      occurrence:
        tag: occurrence
        value: m
    description: List of chemical compounds administered to the host or site where
      sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
      include multiple compounds. For chemical entities of biological interest ontology
      (chebi) (v 163), http://purl.bioontology.org/ontology/chebi
    title: chemical administration
    examples:
    - value: agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22
    - value: agar [CHEBI:2509];2018-05
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - chemical administration
    rank: 17
    is_a: core field
    string_serialization: '{termLabel} {[termID]};{timestamp}'
    slot_uri: MIXS:0000751
    multivalued: false
    alias: chem_administration
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    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)?)?)?)?$
  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
    multivalued: false
    alias: collection_date
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  depth:
    name: depth
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: The vertical distance below local surface, e.g. for sediment or soil
      samples depth is measured from sediment or soil surface, respectively. Depth
      can be reported as an interval for subsurface samples.
    title: depth, meters
    notes:
    - Use modified term
    comments:
    - All depths must be reported in meters. Provide the numerical portion only.
    examples:
    - value: 0 - 0.1
    - value: '1'
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - depth
    rank: 9
    is_a: environment field
    string_serialization: '{float}|{float}-{float}'
    slot_uri: MIXS:0000018
    multivalued: false
    alias: depth
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
    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: HostAssociatedInterface
    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: HostAssociatedInterface
    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: HostAssociatedInterface
    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: HostAssociatedInterface
    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
    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
    rank: 6
    is_a: environment field
    slot_uri: MIXS:0000093
    multivalued: false
    alias: elev
    owner: HostAssociatedInterface
    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
  env_broad_scale:
    name: env_broad_scale
    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)
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 6
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    multivalued: false
    alias: env_broad_scale
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: string
    required: true
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  env_local_scale:
    name: env_local_scale
    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
    rank: 7
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000013
    multivalued: false
    alias: env_local_scale
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: string
    required: true
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  env_medium:
    name: env_medium
    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
    rank: 8
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000014
    multivalued: false
    alias: env_medium
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: sample_id_section
    range: string
    required: true
    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
    multivalued: false
    alias: experimental_factor
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
  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
    multivalued: false
    alias: genetic_mod
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: geo_loc_name
    owner: HostAssociatedInterface
    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
    pattern: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
  gravidity:
    name: gravidity
    annotations:
      expected_value:
        tag: expected_value
        value: gravidity status;timestamp
      occurrence:
        tag: occurrence
        value: '1'
    description: Whether or not subject is gravid, and if yes date due or date post-conception,
      specifying which is used
    title: gravidity
    examples:
    - value: yes;due date:2018-05-11
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - gravidity
    rank: 312
    is_a: core field
    string_serialization: '{boolean};{timestamp}'
    slot_uri: MIXS:0000875
    multivalued: false
    alias: gravidity
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_age:
    name: host_age
    annotations:
      expected_value:
        tag: expected_value
        value: value
      preferred_unit:
        tag: preferred_unit
        value: year, day, hour
      occurrence:
        tag: occurrence
        value: '1'
    description: Age of host at the time of sampling; relevant scale depends on species
      and study, e.g. Could be seconds for amoebae or centuries for trees
    title: host age
    examples:
    - value: 10 days
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host age
    rank: 249
    is_a: core field
    slot_uri: MIXS:0000255
    multivalued: false
    alias: host_age
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_body_habitat:
    name: host_body_habitat
    annotations:
      expected_value:
        tag: expected_value
        value: free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Original body habitat where the sample was obtained from
    title: host body habitat
    examples:
    - value: nasopharynx
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host body habitat
    rank: 319
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000866
    multivalued: false
    alias: host_body_habitat
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_body_product:
    name: host_body_product
    annotations:
      expected_value:
        tag: expected_value
        value: FMA or UBERON
      occurrence:
        tag: occurrence
        value: '1'
    description: Substance produced by the body, e.g. Stool, mucus, where the sample
      was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy
      ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma
      or https://www.ebi.ac.uk/ols/ontologies/uberon
    title: host body product
    examples:
    - value: Portion of mucus [fma66938]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host body product
    rank: 320
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000888
    multivalued: false
    alias: host_body_product
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  host_body_site:
    name: host_body_site
    annotations:
      expected_value:
        tag: expected_value
        value: FMA or UBERON
      occurrence:
        tag: occurrence
        value: '1'
    description: Name of body site where the sample was obtained from, such as a specific
      organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology
      (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,
      please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON
    title: host body site
    examples:
    - value: gill [UBERON:0002535]
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host body site
    rank: 321
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000867
    multivalued: false
    alias: host_body_site
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  host_body_temp:
    name: host_body_temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
      occurrence:
        tag: occurrence
        value: '1'
    description: Core body temperature of the host when sample was collected
    title: host body temperature
    examples:
    - value: 15 degree Celsius
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host body temperature
    rank: 322
    is_a: core field
    slot_uri: MIXS:0000274
    multivalued: false
    alias: host_body_temp
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_color:
    name: host_color
    annotations:
      expected_value:
        tag: expected_value
        value: color
      occurrence:
        tag: occurrence
        value: '1'
    description: The color of host
    title: host color
    examples:
    - value: ''
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host color
    rank: 323
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000260
    multivalued: false
    alias: host_color
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: host_common_name
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_diet:
    name: host_diet
    annotations:
      expected_value:
        tag: expected_value
        value: diet type
      occurrence:
        tag: occurrence
        value: m
    description: Type of diet depending on the host, for animals omnivore, herbivore
      etc., for humans high-fat, meditteranean etc.; can include multiple diet types
    title: host diet
    examples:
    - value: herbivore
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host diet
    rank: 324
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000869
    multivalued: false
    alias: host_diet
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: host_disease_stat
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: host_dry_mass
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_family_relation:
    name: host_family_relation
    annotations:
      expected_value:
        tag: expected_value
        value: relationship type;arbitrary identifier
      occurrence:
        tag: occurrence
        value: m
    description: Familial relationships to other hosts in the same study; can include
      multiple relationships
    title: host family relationship
    examples:
    - value: offspring;Mussel25
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host family relationship
    rank: 325
    is_a: core field
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0000872
    multivalued: false
    alias: host_family_relation
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: host_genotype
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_growth_cond:
    name: host_growth_cond
    annotations:
      expected_value:
        tag: expected_value
        value: PMID,DOI,url or free text
      occurrence:
        tag: occurrence
        value: '1'
    description: Literature reference giving growth conditions of the host
    title: host growth conditions
    examples:
    - value: https://academic.oup.com/icesjms/article/68/2/349/617247
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host growth conditions
    rank: 326
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0000871
    multivalued: false
    alias: host_growth_cond
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: host_height
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  host_last_meal:
    name: host_last_meal
    annotations:
      expected_value:
        tag: expected_value
        value: content;duration
      occurrence:
        tag: occurrence
        value: m
    description: Content of last meal and time since feeding; can include multiple
      values
    title: host last meal
    examples:
    - value: corn feed;P2H
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host last meal
    rank: 327
    is_a: core field
    string_serialization: '{text};{duration}'
    slot_uri: MIXS:0000870
    multivalued: false
    alias: host_last_meal
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: host_length
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    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
    multivalued: false
    alias: host_life_stage
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: host_phenotype
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  host_sex:
    name: host_sex
    annotations:
      expected_value:
        tag: expected_value
        value: enumeration
      occurrence:
        tag: occurrence
        value: '1'
    description: Gender or physical sex of the host.
    title: host sex
    examples:
    - value: non-binary
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host sex
    rank: 328
    is_a: core field
    slot_uri: MIXS:0000811
    multivalued: false
    alias: host_sex
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: host_sex_enum
  host_shape:
    name: host_shape
    annotations:
      expected_value:
        tag: expected_value
        value: shape
      occurrence:
        tag: occurrence
        value: '1'
    description: Morphological shape of host
    title: host shape
    examples:
    - value: round
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host shape
    rank: 329
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000261
    multivalued: false
    alias: host_shape
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_subject_id:
    name: host_subject_id
    annotations:
      expected_value:
        tag: expected_value
        value: unique identifier
      occurrence:
        tag: occurrence
        value: '1'
    description: A unique identifier by which each subject can be referred to, de-identified.
    title: host subject id
    examples:
    - value: MPI123
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host subject id
    rank: 330
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000861
    multivalued: false
    alias: host_subject_id
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: host_subspecf_genlin
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  host_substrate:
    name: host_substrate
    annotations:
      expected_value:
        tag: expected_value
        value: substrate name
      occurrence:
        tag: occurrence
        value: '1'
    description: The growth substrate of the host.
    title: host substrate
    examples:
    - value: rock
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - host substrate
    rank: 331
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000252
    multivalued: false
    alias: host_substrate
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: host_symbiont
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: host_taxid
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: host_tot_mass
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  lat_lon:
    name: lat_lon
    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
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 5
    is_a: environment field
    string_serialization: '{lat lon}'
    slot_uri: MIXS:0000009
    multivalued: false
    alias: lat_lon
    owner: HostAssociatedInterface
    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
    pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$
  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
    multivalued: false
    alias: misc_param
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
      [^;\t\r\x0A]+)$
  organism_count:
    name: organism_count
    annotations:
      expected_value:
        tag: expected_value
        value: organism name;measurement value;enumeration
      preferred_unit:
        tag: preferred_unit
        value: number of cells per cubic meter, number of cells per milliliter, number
          of cells per cubic centimeter
      occurrence:
        tag: occurrence
        value: m
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - organism count
    rank: 30
    is_a: core field
    slot_uri: MIXS:0000103
    multivalued: false
    alias: organism_count
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
    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
    multivalued: false
    alias: oxy_stat_samp
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: OxyStatSampEnum
  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
    multivalued: false
    alias: perturbation
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: salinity
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  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
    multivalued: false
    alias: samp_capt_status
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: samp_capt_status_enum
  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
    multivalued: false
    alias: samp_collec_device
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    recommended: true
  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
    multivalued: false
    alias: samp_collec_method
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
  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
    multivalued: false
    alias: samp_dis_stage
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - HostAssociatedInterface
    - PlantAssociatedInterface
    slot_group: mixs_core_section
    range: samp_dis_stage_enum
  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
    multivalued: false
    alias: samp_mat_process
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
  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
    multivalued: false
    alias: samp_size
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    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
    multivalued: false
    alias: samp_store_dur
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: samp_store_loc
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
  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
    multivalued: false
    alias: samp_store_temp
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    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}'
    multivalued: false
    alias: sample_link
    owner: HostAssociatedInterface
    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
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'
  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
    multivalued: false
    alias: size_frac
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_core_section
    range: string
  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: HostAssociatedInterface
    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
  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
    multivalued: false
    alias: temp
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    slot_group: mixs_section
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
  analysis_type:
    name: analysis_type
    description: Select all the data types associated or available for this biosample
    title: analysis/data type
    examples:
    - value: metagenomics; metabolomics; proteomics
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - MIxS:investigation_type
    rank: 3
    multivalued: true
    alias: analysis_type
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: AnalysisTypeEnum
    required: true
    recommended: false
  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
    multivalued: false
    identifier: true
    alias: samp_name
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    required: true
  source_mat_id:
    name: source_mat_id
    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
    rank: 2
    is_a: nucleic acid sequence source field
    string_serialization: '{text}:{text}'
    slot_uri: MIXS:0000026
    multivalued: false
    alias: source_mat_id
    owner: HostAssociatedInterface
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'