Extension: human-oral (HumanOral)

A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their oral-associated microbiome.

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:0000283	nose_mouth_teeth_throat_disord	* String	History of nose/mouth/teeth/throat disorders; can include multiple disorders
MIXS:0000924	time_last_toothbrush	0..1 String	Specification of the time since last toothbrushing
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: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:0000884	ihmc_medication_code	* Integer	Can include multiple medication codes
MIXS:0000751	chem_administration	* String	List of chemical compounds administered to the host or site where sampling oc...
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: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:0000872	host_fam_rel	* String	Relationships to other hosts in the same study; can include multiple relation...
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:0000317	host_body_mass_index	0..1 String	Body mass index, calculated as weight/(height)squared
MIXS:0000895	ethnicity	* String	A category of people who identify with each other, usually on the basis of pr...
MIXS:0000896	host_occupation	0..1 String	Most frequent job performed by subject
MIXS:0000897	medic_hist_perform	0..1 Boolean	Whether full medical history was collected
MIXS:0000333	host_pulse	0..1 String	Resting pulse, measured as beats per minute
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:0001298	host_symbiont	* String	The taxonomic name of the organism(s) found living in mutualistic, commensali...
MIXS:0000755	samp_store_loc	0..1 String	Location at which sample was stored, usually name of a specific freezer/room
MIXS:0000752	misc_param	* String	Any other measurement performed or parameter collected, that is not listed he...

Aliases

• MIxS-human-oral

Annotations

• use_cases: mouth swab sampling, dental microbiome samples, microbiome of oral swabs, nasal, mouth, throat, teeth, tongue microbiome studies

LinkML Source

Direct

name: HumanOral
annotations:
  use_cases:
    tag: use_cases
    value: mouth swab sampling, dental microbiome samples, microbiome of oral swabs,
      nasal, mouth, throat, teeth, tongue microbiome studies
description: A collection of terms appropriate when collecting samples and sequencing
  samples  obtained from a person to examine their oral-associated microbiome.
title: human-oral
from_schema: https://w3id.org/mixs
aliases:
- MIxS-human-oral
is_a: Extension
slots:
- samp_name
- project_name
- nose_mouth_teeth_throat_disord
- time_last_toothbrush
- host_subject_id
- host_age
- host_sex
- host_disease_stat
- ihmc_medication_code
- chem_administration
- host_body_site
- host_body_product
- host_tot_mass
- host_height
- host_diet
- host_last_meal
- host_fam_rel
- host_genotype
- host_phenotype
- host_body_temp
- host_body_mass_index
- ethnicity
- host_occupation
- medic_hist_perform
- host_pulse
- perturbation
- salinity
- oxy_stat_samp
- temp
- organism_count
- samp_vol_we_dna_ext
- samp_store_temp
- samp_store_dur
- host_symbiont
- samp_store_loc
- misc_param
slot_usage:
  host_age:
    name: host_age
    examples:
    - value: 30 years
  host_body_site:
    name: host_body_site
    examples:
    - value: Epithelium of tongue [fma284658]
  host_body_temp:
    name: host_body_temp
    examples:
    - value: 36.5 degree Celsius
  host_diet:
    name: host_diet
    examples:
    - value: high-fat
  host_disease_stat:
    name: host_disease_stat
    examples:
    - value: measles [DOID:8622]
  host_fam_rel:
    name: host_fam_rel
    examples:
    - value: mother;ID298
  host_genotype:
    name: host_genotype
    examples:
    - value: ST1
  host_height:
    name: host_height
    examples:
    - value: 1.75 meter
  host_last_meal:
    name: host_last_meal
    examples:
    - value: french fries;P5H30M
  host_phenotype:
    name: host_phenotype
    examples:
    - value: Tinnitus [HP:0000360]
  host_subject_id:
    name: host_subject_id
    examples:
    - value: MPI123
  host_symbiont:
    name: host_symbiont
    examples:
    - value: flukeworms
  host_tot_mass:
    name: host_tot_mass
    examples:
    - value: 65 kilogram
  organism_count:
    name: organism_count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
class_uri: MIXS:0016005

Induced

name: HumanOral
annotations:
  use_cases:
    tag: use_cases
    value: mouth swab sampling, dental microbiome samples, microbiome of oral swabs,
      nasal, mouth, throat, teeth, tongue microbiome studies
description: A collection of terms appropriate when collecting samples and sequencing
  samples  obtained from a person to examine their oral-associated microbiome.
title: human-oral
from_schema: https://w3id.org/mixs
aliases:
- MIxS-human-oral
is_a: Extension
slot_usage:
  host_age:
    name: host_age
    examples:
    - value: 30 years
  host_body_site:
    name: host_body_site
    examples:
    - value: Epithelium of tongue [fma284658]
  host_body_temp:
    name: host_body_temp
    examples:
    - value: 36.5 degree Celsius
  host_diet:
    name: host_diet
    examples:
    - value: high-fat
  host_disease_stat:
    name: host_disease_stat
    examples:
    - value: measles [DOID:8622]
  host_fam_rel:
    name: host_fam_rel
    examples:
    - value: mother;ID298
  host_genotype:
    name: host_genotype
    examples:
    - value: ST1
  host_height:
    name: host_height
    examples:
    - value: 1.75 meter
  host_last_meal:
    name: host_last_meal
    examples:
    - value: french fries;P5H30M
  host_phenotype:
    name: host_phenotype
    examples:
    - value: Tinnitus [HP:0000360]
  host_subject_id:
    name: host_subject_id
    examples:
    - value: MPI123
  host_symbiont:
    name: host_symbiont
    examples:
    - value: flukeworms
  host_tot_mass:
    name: host_tot_mass
    examples:
    - value: 65 kilogram
  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: HumanOral
    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: HumanOral
    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
  nose_mouth_teeth_throat_disord:
    name: nose_mouth_teeth_throat_disord
    description: History of nose/mouth/teeth/throat disorders; can include multiple
      disorders. The terms should be chosen from the DO (Human Disease Ontology) at
      http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825),
      mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091),
      or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974)
    title: nose/mouth/teeth/throat disorder
    from_schema: https://w3id.org/mixs
    keywords:
    - disorder
    slot_uri: MIXS:0000283
    alias: nose_mouth_teeth_throat_disord
    owner: HumanOral
    domain_of:
    - HumanOral
    range: string
    multivalued: true
  time_last_toothbrush:
    name: time_last_toothbrush
    description: Specification of the time since last toothbrushing
    title: time since last toothbrushing
    comments:
    - P2H45M does not match ^P(?!$)(\\d+Y)?(\\d+M)?(\\d+W)?(\\d+D)?(T(?=\\d+[HMS])(\\d+H)?(\\d+M)?(\\d+S)?)?$
    - problematic ISO 8601 period validation
    examples:
    - value: PT2H45M
    from_schema: https://w3id.org/mixs
    keywords:
    - time
    slot_uri: MIXS:0000924
    alias: time_last_toothbrush
    owner: HumanOral
    domain_of:
    - HumanOral
    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
  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: HumanOral
    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: 30 years
    from_schema: https://w3id.org/mixs
    keywords:
    - age
    - host
    - host.
    slot_uri: MIXS:0000255
    alias: host_age
    owner: HumanOral
    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_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: HumanOral
    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: measles [DOID:8622]
    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: HumanOral
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    range: string
  ihmc_medication_code:
    name: ihmc_medication_code
    description: Can include multiple medication codes
    title: IHMC medication code
    examples:
    - value: '810'
    from_schema: https://w3id.org/mixs
    keywords:
    - code
    slot_uri: MIXS:0000884
    alias: ihmc_medication_code
    owner: HumanOral
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: integer
    multivalued: true
  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: HumanOral
    domain_of:
    - Agriculture
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  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: Epithelium of tongue [fma284658]
    from_schema: https://w3id.org/mixs
    keywords:
    - body
    - host
    - site
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000867
    alias: host_body_site
    owner: HumanOral
    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: HumanOral
    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: 65 kilogram
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - mass
    - total
    slot_uri: MIXS:0000263
    alias: host_tot_mass
    owner: HumanOral
    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: 1.75 meter
    from_schema: https://w3id.org/mixs
    keywords:
    - height
    - host
    - host.
    slot_uri: MIXS:0000264
    alias: host_height
    owner: HumanOral
    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_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: high-fat
    from_schema: https://w3id.org/mixs
    keywords:
    - diet
    - host
    - host.
    slot_uri: MIXS:0000869
    alias: host_diet
    owner: HumanOral
    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: french fries;P5H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    string_serialization: '{text};{duration}'
    slot_uri: MIXS:0000870
    alias: host_last_meal
    owner: HumanOral
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
    multivalued: true
  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: mother;ID298
    from_schema: https://w3id.org/mixs
    keywords:
    - family
    - host
    - host.
    - relationship
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0000872
    alias: host_fam_rel
    owner: HumanOral
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
    multivalued: true
  host_genotype:
    name: host_genotype
    description: Observed genotype
    title: host genotype
    examples:
    - value: ST1
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000365
    alias: host_genotype
    owner: HumanOral
    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: Tinnitus [HP:0000360]
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000874
    alias: host_phenotype
    owner: HumanOral
    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: 36.5 degree Celsius
    from_schema: https://w3id.org/mixs
    keywords:
    - body
    - host
    - host.
    - temperature
    slot_uri: MIXS:0000274
    alias: host_body_temp
    owner: HumanOral
    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_body_mass_index:
    name: host_body_mass_index
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: kilogram per square meter
    description: Body mass index, calculated as weight/(height)squared
    title: host body-mass index
    examples:
    - value: 22 kilogram per square meter
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000317
    alias: host_body_mass_index
    owner: HumanOral
    domain_of:
    - 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
  ethnicity:
    name: ethnicity
    annotations:
      Expected_value:
        tag: Expected_value
        value: text recommend from Wikipedia list
    description: A category of people who identify with each other, usually on the
      basis of presumed similarities such as a common language, ancestry, history,
      society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups
    title: ethnicity
    examples:
    - value: native american
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000895
    alias: ethnicity
    owner: HumanOral
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
    multivalued: true
  host_occupation:
    name: host_occupation
    description: Most frequent job performed by subject
    title: host occupation
    comments:
    - Couldn't convert host_occupation with value veterinary to integer
    - almost all host_occupation values in the NCBI biosample_set are strings, not
      integers
    examples:
    - value: veterinary
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000896
    alias: host_occupation
    owner: HumanOral
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
  medic_hist_perform:
    name: medic_hist_perform
    description: Whether full medical history was collected
    title: medical history performed
    examples:
    - value: '1'
    from_schema: https://w3id.org/mixs
    keywords:
    - history
    slot_uri: MIXS:0000897
    alias: medic_hist_perform
    owner: HumanOral
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: boolean
  host_pulse:
    name: host_pulse
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: beats per minute
    description: Resting pulse, measured as beats per minute
    title: host pulse
    examples:
    - value: 65 beats per minute
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000333
    alias: host_pulse
    owner: HumanOral
    domain_of:
    - 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
  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: HumanOral
    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: HumanOral
    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: HumanOral
    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: HumanOral
    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: HumanOral
    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: HumanOral
    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: HumanOral
    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: HumanOral
    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
  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: HumanOral
    domain_of:
    - Agriculture
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    multivalued: 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: HumanOral
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
  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: HumanOral
    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:0016005