Extension: host-associated (HostAssociated)

A collection of terms appropriate when collecting samples and sequencing samples obtained from a non-human host, to examine the host-associated microbiome or genome.

Terms

MIXS ID	Name	Cardinality and Range	Description
MIXS:0001107	samp_name	1 String	A local identifier or name that for the material sample used for extracting n...
MIXS:0000092	project_name	1 String	Name of the project within which the sequencing was organized
MIXS:0000094	alt	0..1 recommended String	Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba...
MIXS:0000018	depth	0..1 recommended String	The vertical distance below local surface
MIXS:0000093	elev	0..1 recommended String	Elevation of the sampling site is its height above a fixed reference point, m...
MIXS:0000247	ances_data	0..1 String	Information about either pedigree or other ancestral information description ...
MIXS:0000858	biol_stat	0..1 BiolStatEnum	The level of genome modification
MIXS:0000859	genetic_mod	0..1 String	Genetic modifications of the genome of an organism, which may occur naturally...
MIXS:0000248	host_common_name	0..1 String	Common name of the host
MIXS:0000860	samp_capt_status	0..1 SampCaptStatusEnum	Reason for the sample
MIXS:0000249	samp_dis_stage	0..1 SampDisStageEnum	Stage of the disease at the time of sample collection, e
MIXS:0000250	host_taxid	0..1 String	NCBI taxon id of the host, e
MIXS:0000861	host_subject_id	0..1 String	A unique identifier by which each subject can be referred to, de-identified
MIXS:0000255	host_age	0..1 String	Age of host at the time of sampling; relevant scale depends on species and st...
MIXS:0000251	host_life_stage	0..1 String	Description of life stage of host
MIXS:0000811	host_sex	0..1 String	Gender or physical sex of the host
MIXS:0000031	host_disease_stat	0..1 String	List of diseases with which the host has been diagnosed; can include multiple...
MIXS:0000751	chem_administration	* String	List of chemical compounds administered to the host or site where sampling oc...
MIXS:0000866	host_body_habitat	0..1 String	Original body habitat where the sample was obtained from
MIXS:0000867	host_body_site	0..1 String	Name of body site where the sample was obtained from, such as a specific orga...
MIXS:0000888	host_body_product	0..1 String	Substance produced by the body, e
MIXS:0000263	host_tot_mass	0..1 String	Total mass of the host at collection, the unit depends on host
MIXS:0000264	host_height	0..1 String	The height of subject
MIXS:0000256	host_length	0..1 String	The length of subject
MIXS:0000869	host_diet	* String	Type of diet depending on the host, for animals omnivore, herbivore etc
MIXS:0000870	host_last_meal	* String	Content of last meal and time since feeding; can include multiple values
MIXS:0000871	host_growth_cond	0..1 String	Literature reference giving growth conditions of the host
MIXS:0000252	host_substrate	0..1 String	The growth substrate of the host
MIXS:0000872	host_fam_rel	* String	Relationships to other hosts in the same study; can include multiple relation...
MIXS:0001318	host_subspecf_genlin	* String	Information about the genetic distinctness of the host organism below the sub...
MIXS:0000365	host_genotype	0..1 String	Observed genotype
MIXS:0000874	host_phenotype	0..1 String	Phenotype of human or other host
MIXS:0000274	host_body_temp	0..1 String	Core body temperature of the host when sample was collected
MIXS:0000257	host_dry_mass	0..1 String	Measurement of dry mass
MIXS:0000258	blood_press_diast	0..1 String	Resting diastolic blood pressure, measured as mm mercury
MIXS:0000259	blood_press_syst	0..1 String	Resting systolic blood pressure, measured as mm mercury
MIXS:0000260	host_color	0..1 String	The color of host
MIXS:0000261	host_shape	0..1 String	Morphological shape of host
MIXS:0000875	gravidity	0..1 String	Whether or not subject is gravid, and if yes date due or date post-conception...
MIXS:0000754	perturbation	* String	Type of perturbation, e
MIXS:0000183	salinity	0..1 String	The total concentration of all dissolved salts in a liquid or solid sample
MIXS:0000753	oxy_stat_samp	0..1 OxyStatSampEnum	Oxygenation status of sample
MIXS:0000113	temp	0..1 String	Temperature of the sample at the time of sampling
MIXS:0000103	organism_count	* String	Total cell count of any organism (or group of organisms) per gram, volume or ...
MIXS:0000111	samp_vol_we_dna_ext	0..1 String	Volume (ml) or mass (g) of total collected sample processed for DNA extractio...
MIXS:0000110	samp_store_temp	0..1 String	Temperature at which sample was stored, e
MIXS:0000116	samp_store_dur	0..1 String	Duration for which the sample was stored
MIXS:0000755	samp_store_loc	0..1 String	Location at which sample was stored, usually name of a specific freezer/room
MIXS:0001298	host_symbiont	* String	The taxonomic name of the organism(s) found living in mutualistic, commensali...
MIXS:0000752	misc_param	* String	Any other measurement performed or parameter collected, that is not listed he...

Aliases

• MIxS-host-associated

Annotations

• use_cases: elephant fecal matter or cat oral cavity

LinkML Source

Direct

name: HostAssociated
annotations:
  use_cases:
    tag: use_cases
    value: elephant fecal matter or cat oral cavity
description: A collection of terms appropriate when collecting samples and sequencing
  samples  obtained from a non-human host, to examine the host-associated microbiome
  or genome.
title: host-associated
comments:
- This is a very broad package, intended to capture many kinds of sequences derived
  from the bodies of or derived from an organism. Where possible, please use a more
  specific package. For example, consider using food-animal and animal feed extension
  for sampling of farm animals reared for consumption. For human stool microbiomes,
  consider MIxS-human-gut. Incidental associations of environmental material with
  an organism may also be better served by other packages. For example, nucleic acids
  derived from soil that was sampled from the hoof of a cow may be better described
  by terms from the soil extension; however, soil embedded in a wound on a cow’s leg
  would be best described by terms in this extension
from_schema: https://w3id.org/mixs
aliases:
- MIxS-host-associated
is_a: Extension
slots:
- samp_name
- project_name
- alt
- depth
- elev
- ances_data
- biol_stat
- genetic_mod
- host_common_name
- samp_capt_status
- samp_dis_stage
- host_taxid
- host_subject_id
- host_age
- host_life_stage
- host_sex
- host_disease_stat
- chem_administration
- host_body_habitat
- host_body_site
- host_body_product
- host_tot_mass
- host_height
- host_length
- host_diet
- host_last_meal
- host_growth_cond
- host_substrate
- host_fam_rel
- host_subspecf_genlin
- host_genotype
- host_phenotype
- host_body_temp
- host_dry_mass
- blood_press_diast
- blood_press_syst
- host_color
- host_shape
- gravidity
- perturbation
- salinity
- oxy_stat_samp
- temp
- organism_count
- samp_vol_we_dna_ext
- samp_store_temp
- samp_store_dur
- samp_store_loc
- host_symbiont
- misc_param
slot_usage:
  alt:
    name: alt
    recommended: true
  depth:
    name: depth
    examples:
    - value: 10 meter
    recommended: true
  elev:
    name: elev
    recommended: true
  host_age:
    name: host_age
    examples:
    - value: 10 days
  host_body_habitat:
    name: host_body_habitat
    examples:
    - value: nasopharynx
  host_body_site:
    name: host_body_site
    examples:
    - value: gill [UBERON:0002535]
  host_body_temp:
    name: host_body_temp
    examples:
    - value: 15 degree Celsius
  host_common_name:
    name: host_common_name
    examples:
    - value: human
  host_diet:
    name: host_diet
    examples:
    - value: herbivore
  host_disease_stat:
    name: host_disease_stat
    examples:
    - value: rabies [DOID:11260]
  host_fam_rel:
    name: host_fam_rel
    examples:
    - value: offspring;Mussel25
  host_genotype:
    name: host_genotype
    examples:
    - value: C57BL/6
  host_height:
    name: host_height
    examples:
    - value: 0.1 meter
  host_last_meal:
    name: host_last_meal
    examples:
    - value: corn feed;P2H
  host_life_stage:
    name: host_life_stage
    examples:
    - value: adult
  host_phenotype:
    name: host_phenotype
    examples:
    - value: elongated [PATO:0001154]
  host_subject_id:
    name: host_subject_id
    examples:
    - value: MPI123
  host_symbiont:
    name: host_symbiont
    examples:
    - value: flukeworms
  host_taxid:
    name: host_taxid
    examples:
    - value: '7955'
    string_serialization: '{NCBI taxid}'
  host_tot_mass:
    name: host_tot_mass
    examples:
    - value: 2500 gram
  organism_count:
    name: organism_count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
class_uri: MIXS:0016002

Induced

name: HostAssociated
annotations:
  use_cases:
    tag: use_cases
    value: elephant fecal matter or cat oral cavity
description: A collection of terms appropriate when collecting samples and sequencing
  samples  obtained from a non-human host, to examine the host-associated microbiome
  or genome.
title: host-associated
comments:
- This is a very broad package, intended to capture many kinds of sequences derived
  from the bodies of or derived from an organism. Where possible, please use a more
  specific package. For example, consider using food-animal and animal feed extension
  for sampling of farm animals reared for consumption. For human stool microbiomes,
  consider MIxS-human-gut. Incidental associations of environmental material with
  an organism may also be better served by other packages. For example, nucleic acids
  derived from soil that was sampled from the hoof of a cow may be better described
  by terms from the soil extension; however, soil embedded in a wound on a cow’s leg
  would be best described by terms in this extension
from_schema: https://w3id.org/mixs
aliases:
- MIxS-host-associated
is_a: Extension
slot_usage:
  alt:
    name: alt
    recommended: true
  depth:
    name: depth
    examples:
    - value: 10 meter
    recommended: true
  elev:
    name: elev
    recommended: true
  host_age:
    name: host_age
    examples:
    - value: 10 days
  host_body_habitat:
    name: host_body_habitat
    examples:
    - value: nasopharynx
  host_body_site:
    name: host_body_site
    examples:
    - value: gill [UBERON:0002535]
  host_body_temp:
    name: host_body_temp
    examples:
    - value: 15 degree Celsius
  host_common_name:
    name: host_common_name
    examples:
    - value: human
  host_diet:
    name: host_diet
    examples:
    - value: herbivore
  host_disease_stat:
    name: host_disease_stat
    examples:
    - value: rabies [DOID:11260]
  host_fam_rel:
    name: host_fam_rel
    examples:
    - value: offspring;Mussel25
  host_genotype:
    name: host_genotype
    examples:
    - value: C57BL/6
  host_height:
    name: host_height
    examples:
    - value: 0.1 meter
  host_last_meal:
    name: host_last_meal
    examples:
    - value: corn feed;P2H
  host_life_stage:
    name: host_life_stage
    examples:
    - value: adult
  host_phenotype:
    name: host_phenotype
    examples:
    - value: elongated [PATO:0001154]
  host_subject_id:
    name: host_subject_id
    examples:
    - value: MPI123
  host_symbiont:
    name: host_symbiont
    examples:
    - value: flukeworms
  host_taxid:
    name: host_taxid
    examples:
    - value: '7955'
    string_serialization: '{NCBI taxid}'
  host_tot_mass:
    name: host_tot_mass
    examples:
    - value: 2500 gram
  organism_count:
    name: organism_count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
attributes:
  samp_name:
    name: samp_name
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ''
    description: A local identifier or name that for the material sample used for
      extracting nucleic acids, and subsequent sequencing. It can refer either to
      the original material collected or to any derived sub-samples. It can have any
      format, but we suggest that you make it concise, unique and consistent within
      your lab, and as informative as possible. INSDC requires every sample name from
      a single Submitter to be unique. Use of a globally unique identifier for the
      field source_mat_id is recommended in addition to sample_name
    title: sample name
    examples:
    - value: ISDsoil1
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    slot_uri: MIXS:0001107
    alias: samp_name
    owner: HostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: true
  project_name:
    name: project_name
    description: Name of the project within which the sequencing was organized
    title: project name
    examples:
    - value: Forest soil metagenome
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - project
    slot_uri: MIXS:0000092
    alias: project_name
    owner: HostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: true
  alt:
    name: alt
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: 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
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000094
    alias: alt
    owner: HostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - HostAssociated
    - MiscellaneousNaturalOrArtificialEnvironment
    - SymbiontAssociated
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  depth:
    name: depth
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: The vertical distance below local surface. 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
    examples:
    - value: 10 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - depth
    slot_uri: MIXS:0000018
    alias: depth
    owner: HostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  elev:
    name: elev
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    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
    examples:
    - value: 100 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - elevation
    slot_uri: MIXS:0000093
    alias: elev
    owner: HostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - HostAssociated
    - HydrocarbonResourcesCores
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - Water
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  ances_data:
    name: ances_data
    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/mixs
    slot_uri: MIXS:0000247
    alias: ances_data
    owner: HostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    range: string
  biol_stat:
    name: biol_stat
    description: The level of genome modification
    title: biological status
    examples:
    - value: natural
    from_schema: https://w3id.org/mixs
    keywords:
    - status
    slot_uri: MIXS:0000858
    alias: biol_stat
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - PlantAssociated
    range: BiolStatEnum
  genetic_mod:
    name: genetic_mod
    annotations:
      Expected_value:
        tag: Expected_value
        value: PMID, DOI, URL or text
    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/mixs
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000859
    alias: genetic_mod
    owner: HostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - PlantAssociated
    range: string
  host_common_name:
    name: host_common_name
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ''
    description: Common name of the host
    title: host common name
    examples:
    - value: human
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000248
    alias: host_common_name
    owner: HostAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
  samp_capt_status:
    name: samp_capt_status
    description: Reason for the sample
    title: sample capture status
    examples:
    - value: farm sample
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - status
    slot_uri: MIXS:0000860
    alias: samp_capt_status
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - PlantAssociated
    range: SampCaptStatusEnum
  samp_dis_stage:
    name: samp_dis_stage
    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/mixs
    keywords:
    - disease
    - sample
    slot_uri: MIXS:0000249
    alias: samp_dis_stage
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - PlantAssociated
    range: SampDisStageEnum
  host_taxid:
    name: host_taxid
    annotations:
      Expected_value:
        tag: Expected_value
        value: NCBI taxon identifier
    description: NCBI taxon id of the host, e.g. 9606
    title: host taxid
    examples:
    - value: '7955'
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - taxon
    string_serialization: '{NCBI taxid}'
    slot_uri: MIXS:0000250
    alias: host_taxid
    owner: HostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
  host_subject_id:
    name: host_subject_id
    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/mixs
    keywords:
    - host
    - host.
    - identifier
    slot_uri: MIXS:0000861
    alias: host_subject_id
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
  host_age:
    name: host_age
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: year, day, hour
    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/mixs
    keywords:
    - age
    - host
    - host.
    slot_uri: MIXS:0000255
    alias: host_age
    owner: HostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_life_stage:
    name: host_life_stage
    annotations:
      Expected_value:
        tag: Expected_value
        value: stage
    description: Description of life stage of host
    title: host life stage
    examples:
    - value: adult
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - life
    slot_uri: MIXS:0000251
    alias: host_life_stage
    owner: HostAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
  host_sex:
    name: host_sex
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration
    description: Gender or physical sex of the host
    title: host sex
    comments:
    - example of non-binary from Excel sheets does not match any of the enumerated
      values
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    string_serialization: '[female|hermaphrodite|non-binary|male|transgender|transgender
      (female to male)|transgender (male to female)

      |undeclared]'
    slot_uri: MIXS:0000811
    alias: host_sex
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    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]
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - disease
    - host
    - host.
    - status
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000031
    alias: host_disease_stat
    owner: HostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    range: string
  chem_administration:
    name: chem_administration
    annotations:
      Expected_value:
        tag: Expected_value
        value: CHEBI;timestamp
    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];2018-05-11T20:00Z
    from_schema: https://w3id.org/mixs
    keywords:
    - administration
    string_serialization: '{termLabel} [{termID}];{timestamp}'
    slot_uri: MIXS:0000751
    alias: chem_administration
    owner: HostAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  host_body_habitat:
    name: host_body_habitat
    description: Original body habitat where the sample was obtained from
    title: host body habitat
    examples:
    - value: nasopharynx
    from_schema: https://w3id.org/mixs
    keywords:
    - body
    - habitat
    - host
    - host.
    slot_uri: MIXS:0000866
    alias: host_body_habitat
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  host_body_site:
    name: host_body_site
    annotations:
      Expected_value:
        tag: Expected_value
        value: FMA or UBERON
    description: Name of body site where the sample was obtained from, such as a specific
      organ or tissue (tongue, lung etc...). Use terms from the foundational model
      of anatomy ontology (fma) or the Uber-anatomy ontology (UBERON)
    title: host body site
    examples:
    - value: gill [UBERON:0002535]
    from_schema: https://w3id.org/mixs
    keywords:
    - body
    - host
    - site
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000867
    alias: host_body_site
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
  host_body_product:
    name: host_body_product
    annotations:
      Expected_value:
        tag: Expected_value
        value: FMA or UBERON
    description: Substance produced by the body, e.g. Stool, mucus, where the sample
      was obtained from. Use terms from the foundational model of anatomy ontology
      (fma) or Uber-anatomy ontology (UBERON)
    title: host body product
    examples:
    - value: mucus [FMA:66938]
    from_schema: https://w3id.org/mixs
    keywords:
    - body
    - host
    - host.
    - product
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000888
    alias: host_body_product
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
  host_tot_mass:
    name: host_tot_mass
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: kilogram, gram
    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/mixs
    keywords:
    - host
    - host.
    - mass
    - total
    slot_uri: MIXS:0000263
    alias: host_tot_mass
    owner: HostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_height:
    name: host_height
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: centimeter, millimeter, meter
    description: The height of subject
    title: host height
    examples:
    - value: 0.1 meter
    from_schema: https://w3id.org/mixs
    keywords:
    - height
    - host
    - host.
    slot_uri: MIXS:0000264
    alias: host_height
    owner: HostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_length:
    name: host_length
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: centimeter, millimeter, meter
    description: The length of subject
    title: host length
    examples:
    - value: 1 meter
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - length
    slot_uri: MIXS:0000256
    alias: host_length
    owner: HostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_diet:
    name: host_diet
    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/mixs
    keywords:
    - diet
    - host
    - host.
    slot_uri: MIXS:0000869
    alias: host_diet
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
    multivalued: true
  host_last_meal:
    name: host_last_meal
    annotations:
      Expected_value:
        tag: Expected_value
        value: content;duration
    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/mixs
    keywords:
    - host
    - host.
    string_serialization: '{text};{duration}'
    slot_uri: MIXS:0000870
    alias: host_last_meal
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
    multivalued: true
  host_growth_cond:
    name: host_growth_cond
    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/mixs
    keywords:
    - condition
    - growth
    - host
    - host.
    slot_uri: MIXS:0000871
    alias: host_growth_cond
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: true
  host_substrate:
    name: host_substrate
    description: The growth substrate of the host
    title: host substrate
    examples:
    - value: rock
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000252
    alias: host_substrate
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  host_fam_rel:
    name: host_fam_rel
    annotations:
      Expected_value:
        tag: Expected_value
        value: relationship type;arbitrary identifier
    description: 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/mixs
    keywords:
    - family
    - host
    - host.
    - relationship
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0000872
    alias: host_fam_rel
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
    multivalued: true
  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
    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/mixs
    keywords:
    - host
    - host.
    - lineage
    string_serialization: '{rank name}:{text}'
    slot_uri: MIXS:0001318
    alias: host_subspecf_genlin
    owner: HostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    range: string
    multivalued: true
  host_genotype:
    name: host_genotype
    description: Observed genotype
    title: host genotype
    examples:
    - value: C57BL/6
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000365
    alias: host_genotype
    owner: HostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
  host_phenotype:
    name: host_phenotype
    annotations:
      Expected_value:
        tag: Expected_value
        value: PATO or HP
    description: Phenotype of human or other host. Use terms from the phenotypic quality
      ontology (pato) or the Human Phenotype Ontology (HP)
    title: host phenotype
    examples:
    - value: elongated [PATO:0001154]
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000874
    alias: host_phenotype
    owner: HostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
  host_body_temp:
    name: host_body_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    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/mixs
    keywords:
    - body
    - host
    - host.
    - temperature
    slot_uri: MIXS:0000274
    alias: host_body_temp
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_dry_mass:
    name: host_dry_mass
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: kilogram, gram
    description: Measurement of dry mass
    title: host dry mass
    examples:
    - value: 500 gram
    from_schema: https://w3id.org/mixs
    keywords:
    - dry
    - host
    - host.
    - mass
    slot_uri: MIXS:0000257
    alias: host_dry_mass
    owner: HostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  blood_press_diast:
    name: blood_press_diast
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: millimeter mercury
    description: Resting diastolic blood pressure, measured as mm mercury
    title: host blood pressure diastolic
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - pressure
    slot_uri: MIXS:0000258
    alias: blood_press_diast
    owner: HostAssociated
    domain_of:
    - HostAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  blood_press_syst:
    name: blood_press_syst
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: millimeter mercury
    description: Resting systolic blood pressure, measured as mm mercury
    title: host blood pressure systolic
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - pressure
    slot_uri: MIXS:0000259
    alias: blood_press_syst
    owner: HostAssociated
    domain_of:
    - HostAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_color:
    name: host_color
    description: The color of host
    title: host color
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000260
    alias: host_color
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  host_shape:
    name: host_shape
    description: Morphological shape of host
    title: host shape
    examples:
    - value: round
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000261
    alias: host_shape
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  gravidity:
    name: gravidity
    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/mixs
    string_serialization: '{boolean};{timestamp}'
    slot_uri: MIXS:0000875
    alias: gravidity
    owner: HostAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  perturbation:
    name: perturbation
    annotations:
      Expected_value:
        tag: Expected_value
        value: perturbation type name;perturbation interval and duration
    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/mixs
    keywords:
    - perturbation
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000754
    alias: perturbation
    owner: HostAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  salinity:
    name: salinity
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: practical salinity unit, percentage
    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/mixs
    keywords:
    - salinity
    slot_uri: MIXS:0000183
    alias: salinity
    owner: HostAssociated
    domain_of:
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  oxy_stat_samp:
    name: oxy_stat_samp
    description: Oxygenation status of sample
    title: oxygenation status of sample
    examples:
    - value: aerobic
    from_schema: https://w3id.org/mixs
    keywords:
    - oxygen
    - sample
    - status
    slot_uri: MIXS:0000753
    alias: oxy_stat_samp
    owner: HostAssociated
    domain_of:
    - Agriculture
    - Air
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: OxyStatSampEnum
  temp:
    name: temp
    annotations:
      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
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - temperature
    slot_uri: MIXS:0000113
    alias: temp
    owner: HostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  organism_count:
    name: organism_count
    annotations:
      Expected_value:
        tag: Expected_value
        value: organism name;measurement value;enumeration
    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/mixs
    keywords:
    - count
    - organism
    string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
    slot_uri: MIXS:0000103
    alias: organism_count
    owner: HostAssociated
    domain_of:
    - Agriculture
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  samp_vol_we_dna_ext:
    name: samp_vol_we_dna_ext
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milliliter, gram, milligram, square centimeter
    description: 'Volume (ml) or mass (g) of total collected sample processed for
      DNA extraction. Note: total sample collected should be entered under the term
      Sample Size (MIXS:0000001)'
    title: sample volume or weight for DNA extraction
    examples:
    - value: 1500 milliliter
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - dna
    - sample
    - volume
    - weight
    slot_uri: MIXS:0000111
    alias: samp_vol_we_dna_ext
    owner: HostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_store_temp:
    name: samp_store_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature at which sample was stored, e.g. -80 degree Celsius
    title: sample storage temperature
    examples:
    - value: -80 degree Celsius
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - storage
    - temperature
    slot_uri: MIXS:0000110
    alias: samp_store_temp
    owner: HostAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_store_dur:
    name: samp_store_dur
    description: Duration for which the sample was stored. Indicate the duration for
      which the sample was stored written in ISO 8601 format
    title: sample storage duration
    examples:
    - value: P1Y6M
    from_schema: https://w3id.org/mixs
    keywords:
    - duration
    - period
    - sample
    - storage
    slot_uri: MIXS:0000116
    alias: samp_store_dur
    owner: HostAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
    structured_pattern:
      syntax: ^{duration}$
      interpolated: true
      partial_match: true
  samp_store_loc:
    name: samp_store_loc
    annotations:
      Expected_value:
        tag: Expected_value
        value: location name
    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/mixs
    keywords:
    - location
    - sample
    - storage
    slot_uri: MIXS:0000755
    alias: samp_store_loc
    owner: HostAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
  host_symbiont:
    name: host_symbiont
    annotations:
      Expected_value:
        tag: Expected_value
        value: species name or common name
    description: The taxonomic name of the organism(s) found living in mutualistic,
      commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont
      can have its own symbionts. For example, parasites may have hyperparasites (=parasites
      of the parasite)
    title: observed host symbionts
    examples:
    - value: flukeworms
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - observed
    - symbiosis
    slot_uri: MIXS:0001298
    alias: host_symbiont
    owner: HostAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    multivalued: true
  misc_param:
    name: misc_param
    annotations:
      Expected_value:
        tag: Expected_value
        value: parameter name;measurement value
    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/mixs
    keywords:
    - parameter
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    alias: misc_param
    owner: HostAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
class_uri: MIXS:0016002