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Extension: human-associated (HumanAssociated)

A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their human-associated microbiome or genome, that does not have a specific extension (e.g., skin, gut, vaginal).

Terms

MIXS ID Name Cardinality and Range Description
MIXS:0001107 samp_name 1..1
String		 A local identifier or name that for the material sample used for extracting n...
MIXS:0000092 project_name 1..1
String		 Name of the project within which the sequencing was organized
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 0..*
Integer		 Can include multiple medication codes
MIXS:0000751 chem_administration 0..*
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 0..*
String		 Type of diet depending on the host, for animals omnivore, herbivore etc
MIXS:0000870 host_last_meal 0..*
String		 Content of last meal and time since feeding; can include multiple values
MIXS:0000872 host_fam_rel 0..*
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:0000262 smoker 0..1
Boolean		 Specification of smoking status
MIXS:0000265 host_hiv_stat 0..1
String		 HIV status of subject, if yes HAART initiation status should also be indicate...
MIXS:0000894 drug_usage 0..*
String		 Any drug used by subject and the frequency of usage; can include multiple dru...
MIXS:0000317 host_body_mass_index 0..1
String		 Body mass index, calculated as weight/(height)squared
MIXS:0000266 diet_last_six_month 0..1
String		 Specification of major diet changes in the last six months, if yes the change...
MIXS:0000295 weight_loss_3_month 0..1
String		 Specification of weight loss in the last three months, if yes should be furth...
MIXS:0000895 ethnicity 0..*
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:0000267 pet_farm_animal 0..*
String		 Specification of presence of pets or farm animals in the environment of subje...
MIXS:0000268 travel_out_six_month 0..*
String		 Specification of the countries travelled in the last six months; can include ...
MIXS:0000326 twin_sibling 0..1
Boolean		 Specification of twin sibling presence
MIXS:0000897 medic_hist_perform 0..1
Boolean		 Whether full medical history was collected
MIXS:0000898 study_complt_stat 0..1
String		 Specification of study completion status, if no the reason should be specifie...
MIXS:0000269 pulmonary_disord 0..*
String		 History of pulmonary disorders; can include multiple disorders
MIXS:0000270 nose_throat_disord 0..*
String		 History of nose-throat disorders; can include multiple disorders, The terms ...
MIXS:0000271 blood_blood_disord 0..*
String		 History of blood disorders; can include multiple disorders
MIXS:0000333 host_pulse 0..1
String		 Resting pulse, measured as beats per minute
MIXS:0000272 gestation_state 0..1
String		 Specification of the gestation state
MIXS:0000273 maternal_health_stat 0..1
String		 Specification of the maternal health status
MIXS:0000275 foetal_health_stat 0..1
String		 Specification of foetal health status, should also include abortion
MIXS:0000276 amniotic_fluid_color 0..1
String		 Specification of the color of the amniotic fluid sample
MIXS:0000277 kidney_disord 0..*
String		 History of kidney disorders; can include multiple disorders
MIXS:0000278 urogenit_tract_disor 0..*
String		 History of urogenital tract disorders; can include multiple disorders
MIXS:0000899 urine_collect_meth 0..1
UrineCollectMethEnum		 Specification of urine collection method
MIXS:0000754 perturbation 0..*
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 0..*
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 0..*
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 0..*
String		 Any other measurement performed or parameter collected, that is not listed he...

Aliases

  • MIxS-human-associated

Annotations

  • use_cases: blood samples or biopsy samples.

LinkML Source

Direct

name: HumanAssociated
annotations:
  use_cases:
    tag: use_cases
    value: blood samples or biopsy samples.
description: A collection of terms appropriate when collecting samples and sequencing
  samples  obtained from a person to examine their human-associated microbiome or
  genome,  that does not have a specific extension (e.g., skin, gut, vaginal).
title: human-associated
comments:
- For stool samples use MIxS-human-gut extension.
from_schema: https://w3id.org/mixs
aliases:
- MIxS-human-associated
is_a: Extension
slots:
- samp_name
- project_name
- 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
- smoker
- host_hiv_stat
- drug_usage
- host_body_mass_index
- diet_last_six_month
- weight_loss_3_month
- ethnicity
- host_occupation
- pet_farm_animal
- travel_out_six_month
- twin_sibling
- medic_hist_perform
- study_complt_stat
- pulmonary_disord
- nose_throat_disord
- blood_blood_disord
- host_pulse
- gestation_state
- maternal_health_stat
- foetal_health_stat
- amniotic_fluid_color
- kidney_disord
- urogenit_tract_disor
- urine_collect_meth
- 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
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
  host_body_site:
    name: host_body_site
    examples:
    - value: Lung parenchyma [fma27360]
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
  host_body_temp:
    name: host_body_temp
    examples:
    - value: 36.5 degree Celsius
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
  host_diet:
    name: host_diet
    examples:
    - value: high-fat
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
  host_disease_stat:
    name: host_disease_stat
    examples:
    - value: measles [DOID:8622]
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
  host_fam_rel:
    name: host_fam_rel
    examples:
    - value: mother;ID298
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
  host_genotype:
    name: host_genotype
    examples:
    - value: ST1
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
  host_height:
    name: host_height
    examples:
    - value: 1.75 meter
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
  host_last_meal:
    name: host_last_meal
    examples:
    - value: french fries;P5H30M
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
  host_phenotype:
    name: host_phenotype
    examples:
    - value: Tinnitus [HP:0000360]
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
  host_subject_id:
    name: host_subject_id
    examples:
    - value: MPI123
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
  host_symbiont:
    name: host_symbiont
    examples:
    - value: flukeworms
    domain_of:
    - Agriculture
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
  host_tot_mass:
    name: host_tot_mass
    examples:
    - value: 65 kilogram
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
  organism_count:
    name: organism_count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    domain_of:
    - Agriculture
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
class_uri: MIXS:0016003

Induced

name: HumanAssociated
annotations:
  use_cases:
    tag: use_cases
    value: blood samples or biopsy samples.
description: A collection of terms appropriate when collecting samples and sequencing
  samples  obtained from a person to examine their human-associated microbiome or
  genome,  that does not have a specific extension (e.g., skin, gut, vaginal).
title: human-associated
comments:
- For stool samples use MIxS-human-gut extension.
from_schema: https://w3id.org/mixs
aliases:
- MIxS-human-associated
is_a: Extension
slot_usage:
  host_age:
    name: host_age
    examples:
    - value: 30 years
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
  host_body_site:
    name: host_body_site
    examples:
    - value: Lung parenchyma [fma27360]
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
  host_body_temp:
    name: host_body_temp
    examples:
    - value: 36.5 degree Celsius
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
  host_diet:
    name: host_diet
    examples:
    - value: high-fat
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
  host_disease_stat:
    name: host_disease_stat
    examples:
    - value: measles [DOID:8622]
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
  host_fam_rel:
    name: host_fam_rel
    examples:
    - value: mother;ID298
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
  host_genotype:
    name: host_genotype
    examples:
    - value: ST1
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
  host_height:
    name: host_height
    examples:
    - value: 1.75 meter
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
  host_last_meal:
    name: host_last_meal
    examples:
    - value: french fries;P5H30M
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
  host_phenotype:
    name: host_phenotype
    examples:
    - value: Tinnitus [HP:0000360]
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
  host_subject_id:
    name: host_subject_id
    examples:
    - value: MPI123
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
  host_symbiont:
    name: host_symbiont
    examples:
    - value: flukeworms
    domain_of:
    - Agriculture
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
  host_tot_mass:
    name: host_tot_mass
    examples:
    - value: 65 kilogram
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
  organism_count:
    name: organism_count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    domain_of:
    - Agriculture
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
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: HumanAssociated
    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: HumanAssociated
    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
  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
    slot_uri: MIXS:0000861
    alias: host_subject_id
    owner: HumanAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
  host_age:
    name: host_age
    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
    slot_uri: MIXS:0000255
    alias: host_age
    owner: HumanAssociated
    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: HumanAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
  host_disease_stat:
    name: host_disease_stat
    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]
    from_schema: https://w3id.org/mixs
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000031
    alias: host_disease_stat
    owner: HumanAssociated
    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
    multivalued: true
    alias: ihmc_medication_code
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: integer
  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
    multivalued: true
    alias: chem_administration
    owner: HumanAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
  host_body_site:
    name: host_body_site
    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: Lung parenchyma [fma27360]
    from_schema: https://w3id.org/mixs
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000867
    alias: host_body_site
    owner: HumanAssociated
    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: HumanAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
  host_tot_mass:
    name: host_tot_mass
    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
    slot_uri: MIXS:0000263
    alias: host_tot_mass
    owner: HumanAssociated
    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
    description: The height of subject
    title: host height
    examples:
    - value: 1.75 meter
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000264
    alias: host_height
    owner: HumanAssociated
    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
    slot_uri: MIXS:0000869
    multivalued: true
    alias: host_diet
    owner: HumanAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
  host_last_meal:
    name: host_last_meal
    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
    string_serialization: '{text};{duration}'
    slot_uri: MIXS:0000870
    multivalued: true
    alias: host_last_meal
    owner: HumanAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
  host_fam_rel:
    name: host_fam_rel
    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
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0000872
    multivalued: true
    alias: host_fam_rel
    owner: HumanAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
  host_genotype:
    name: host_genotype
    description: Observed genotype
    title: host genotype
    examples:
    - value: ST1
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000365
    alias: host_genotype
    owner: HumanAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
  host_phenotype:
    name: host_phenotype
    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
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000874
    alias: host_phenotype
    owner: HumanAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
  host_body_temp:
    name: host_body_temp
    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
    slot_uri: MIXS:0000274
    alias: host_body_temp
    owner: HumanAssociated
    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
  smoker:
    name: smoker
    description: Specification of smoking status
    title: smoker
    examples:
    - value: 'yes'
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000262
    alias: smoker
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: boolean
  host_hiv_stat:
    name: host_hiv_stat
    annotations:
      Expected_value:
        tag: Expected_value
        value: HIV status;HAART initiation status
    description: HIV status of subject, if yes HAART initiation status should also
      be indicated as [YES or NO]
    title: host HIV status
    examples:
    - value: yes;yes
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - status
    string_serialization: '{boolean};{boolean}'
    slot_uri: MIXS:0000265
    alias: host_hiv_stat
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  drug_usage:
    name: drug_usage
    annotations:
      Expected_value:
        tag: Expected_value
        value: drug name;frequency
    description: Any drug used by subject and the frequency of usage; can include
      multiple drugs used
    title: drug usage
    examples:
    - value: Lipitor;2/day
    from_schema: https://w3id.org/mixs
    keywords:
    - drug
    - use
    string_serialization: '{text};{integer}/[year|month|week|day|hour]'
    slot_uri: MIXS:0000894
    multivalued: true
    alias: drug_usage
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  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: HumanAssociated
    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
  diet_last_six_month:
    name: diet_last_six_month
    annotations:
      Expected_value:
        tag: Expected_value
        value: diet change;current diet
    description: Specification of major diet changes in the last six months, if yes
      the change should be specified
    title: major diet change in last six months
    examples:
    - value: yes;vegetarian diet
    from_schema: https://w3id.org/mixs
    keywords:
    - diet
    - months
    string_serialization: '{boolean};{text}'
    slot_uri: MIXS:0000266
    alias: diet_last_six_month
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  weight_loss_3_month:
    name: weight_loss_3_month
    annotations:
      Expected_value:
        tag: Expected_value
        value: weight loss specification;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: kilogram, gram
    description: Specification of weight loss in the last three months, if yes should
      be further specified to include amount of weight loss
    title: weight loss in last three months
    examples:
    - value: yes;5 kilogram
    from_schema: https://w3id.org/mixs
    keywords:
    - months
    - weight
    string_serialization: '{boolean};{float} {unit}'
    slot_uri: MIXS:0000295
    alias: weight_loss_3_month
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  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
    string_serialization: '{text}'
    slot_uri: MIXS:0000895
    multivalued: true
    alias: ethnicity
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
  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: HumanAssociated
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
  pet_farm_animal:
    name: pet_farm_animal
    annotations:
      Expected_value:
        tag: Expected_value
        value: presence status;type of animal or pet
    description: Specification of presence of pets or farm animals in the environment
      of subject, if yes the animals should be specified; can include multiple animals
      present
    title: presence of pets or farm animals
    examples:
    - value: yes; 5 cats
    from_schema: https://w3id.org/mixs
    keywords:
    - animal
    - farm
    - presence
    string_serialization: '{boolean};{text}'
    slot_uri: MIXS:0000267
    multivalued: true
    alias: pet_farm_animal
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  travel_out_six_month:
    name: travel_out_six_month
    annotations:
      Expected_value:
        tag: Expected_value
        value: country name
    description: Specification of the countries travelled in the last six months;
      can include multiple travels
    title: travel outside the country in last six months
    from_schema: https://w3id.org/mixs
    keywords:
    - months
    string_serialization: '{text}'
    slot_uri: MIXS:0000268
    multivalued: true
    alias: travel_out_six_month
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  twin_sibling:
    name: twin_sibling
    description: Specification of twin sibling presence
    title: twin sibling presence
    examples:
    - value: 'yes'
    from_schema: https://w3id.org/mixs
    keywords:
    - presence
    slot_uri: MIXS:0000326
    alias: twin_sibling
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: boolean
  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: HumanAssociated
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: boolean
  study_complt_stat:
    name: study_complt_stat
    annotations:
      Expected_value:
        tag: Expected_value
        value: YES or NO due to (1)adverse event (2) non-compliance (3) lost to follow
          up (4)other-specify
    description: Specification of study completion status, if no the reason should
      be specified
    title: study completion status
    examples:
    - value: no;non-compliance
    from_schema: https://w3id.org/mixs
    keywords:
    - status
    string_serialization: '{boolean};[adverse event|non-compliance|lost to follow
      up|other-specify]'
    slot_uri: MIXS:0000898
    alias: study_complt_stat
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  pulmonary_disord:
    name: pulmonary_disord
    description: History of pulmonary disorders; can include multiple disorders. The
      terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
      lung disease (https://disease-ontology.org/?id=DOID:850)
    title: lung/pulmonary disorder
    from_schema: https://w3id.org/mixs
    keywords:
    - disorder
    slot_uri: MIXS:0000269
    multivalued: true
    alias: pulmonary_disord
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  nose_throat_disord:
    name: nose_throat_disord
    description: History of nose-throat disorders; can include multiple disorders,  The
      terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
      lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory
      tract disease (https://disease-ontology.org/?id=DOID:974)
    title: nose throat disorder
    from_schema: https://w3id.org/mixs
    keywords:
    - disorder
    slot_uri: MIXS:0000270
    multivalued: true
    alias: nose_throat_disord
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  blood_blood_disord:
    name: blood_blood_disord
    description: History of blood disorders; can include multiple disorders.  The
      terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
      hematopoietic system disease (https://disease-ontology.org/?id=DOID:74)
    title: blood/blood disorder
    from_schema: https://w3id.org/mixs
    keywords:
    - disorder
    slot_uri: MIXS:0000271
    multivalued: true
    alias: blood_blood_disord
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  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: HumanAssociated
    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
  gestation_state:
    name: gestation_state
    description: Specification of the gestation state
    title: amniotic fluid/gestation state
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000272
    alias: gestation_state
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  maternal_health_stat:
    name: maternal_health_stat
    description: Specification of the maternal health status
    title: amniotic fluid/maternal health status
    from_schema: https://w3id.org/mixs
    keywords:
    - status
    slot_uri: MIXS:0000273
    alias: maternal_health_stat
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  foetal_health_stat:
    name: foetal_health_stat
    description: Specification of foetal health status, should also include abortion
    title: amniotic fluid/foetal health status
    from_schema: https://w3id.org/mixs
    keywords:
    - status
    slot_uri: MIXS:0000275
    alias: foetal_health_stat
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  amniotic_fluid_color:
    name: amniotic_fluid_color
    description: Specification of the color of the amniotic fluid sample
    title: amniotic fluid/color
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000276
    alias: amniotic_fluid_color
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  kidney_disord:
    name: kidney_disord
    description: History of kidney disorders; can include multiple disorders. The
      terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
      kidney disease (https://disease-ontology.org/?id=DOID:557)
    title: urine/kidney disorder
    from_schema: https://w3id.org/mixs
    keywords:
    - disorder
    slot_uri: MIXS:0000277
    multivalued: true
    alias: kidney_disord
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  urogenit_tract_disor:
    name: urogenit_tract_disor
    description: History of urogenital tract disorders; can include multiple disorders.
      The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
      urinary system disease (https://disease-ontology.org/?id=DOID:18)
    title: urine/urogenital tract disorder
    from_schema: https://w3id.org/mixs
    keywords:
    - disorder
    slot_uri: MIXS:0000278
    multivalued: true
    alias: urogenit_tract_disor
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: string
  urine_collect_meth:
    name: urine_collect_meth
    description: Specification of urine collection method
    title: urine/collection method
    examples:
    - value: catheter
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    slot_uri: MIXS:0000899
    alias: urine_collect_meth
    owner: HumanAssociated
    domain_of:
    - HumanAssociated
    range: UrineCollectMethEnum
  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
    multivalued: true
    alias: perturbation
    owner: HumanAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
  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: HumanAssociated
    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: HumanAssociated
    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: HumanAssociated
    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
    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
    string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
    slot_uri: MIXS:0000103
    multivalued: true
    alias: organism_count
    owner: HumanAssociated
    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
  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: HumanAssociated
    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: HumanAssociated
    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: HumanAssociated
    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
    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
    string_serialization: '{text}'
    slot_uri: MIXS:0001298
    multivalued: true
    alias: host_symbiont
    owner: HumanAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
  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
    string_serialization: '{text}'
    slot_uri: MIXS:0000755
    alias: samp_store_loc
    owner: HumanAssociated
    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
    multivalued: true
    alias: misc_param
    owner: HumanAssociated
    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
class_uri: MIXS:0016003