Extension: symbiont-associated (SymbiontAssociated)

A collection of terms appropriate when collecting samples and sequencing samples obtained from an organism that lives in close association with any other organism(s).

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:0000009	lat_lon	1 String	The geographical origin of the sample as defined by latitude and longitude
MIXS:0000010	geo_loc_name	1 String	The geographical origin of the sample as defined by the country or sea name f...
MIXS:0000011	collection_date	1 Datetime	The time of sampling, either as an instance (single point in time) or interva...
MIXS:0000094	alt	0..1 recommended String	Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba...
MIXS:0000018	depth	0..1 recommended String	The vertical distance below local surface
MIXS:0000093	elev	0..1 recommended String	Elevation of the sampling site is its height above a fixed reference point, m...
MIXS:0000861	host_subject_id	0..1 String	A unique identifier by which each subject can be referred to, de-identified
MIXS:0000248	host_common_name	0..1 String	Common name of the host
MIXS:0000250	host_taxid	0..1 String	NCBI taxon id of the host, e
MIXS:0000026	source_mat_id	* String	A unique identifier assigned to a material sample (as defined by http://rs
MIXS:0001315	host_dependence	1 HostDependenceEnum	Type of host dependence for the symbiotic host organism to its host
MIXS:0001307	type_of_symbiosis	0..1 recommended TypeOfSymbiosisEnum	Type of biological interaction established between the symbiotic host organis...
MIXS:0001300	sym_life_cycle_type	1 SymLifeCycleTypeEnum	Type of life cycle of the symbiotic host species (the thing being sampled)
MIXS:0000251	host_life_stage	1 String	Description of life stage of host
MIXS:0000255	host_age	0..1 String	Age of host at the time of sampling; relevant scale depends on species and st...
MIXS:0000862	urobiom_sex	0..1 UrobiomSexEnum	Physical sex of the host
MIXS:0001312	mode_transmission	0..1 recommended ModeTransmissionEnum	The process through which the symbiotic host organism entered the host from w...
MIXS:0001316	route_transmission	0..1 RouteTransmissionEnum	Description of path taken by the symbiotic host organism being sampled in ord...
MIXS:0000866	host_body_habitat	0..1 String	Original body habitat where the sample was obtained from
MIXS:0000867	host_body_site	0..1 String	Name of body site where the sample was obtained from, such as a specific orga...
MIXS:0000888	host_body_product	0..1 String	Substance produced by the body, e
MIXS:0000263	host_tot_mass	0..1 String	Total mass of the host at collection, the unit depends on host
MIXS:0000264	host_height	0..1 String	The height of subject
MIXS:0000256	host_length	0..1 String	The length of subject
MIXS:0000871	host_growth_cond	0..1 String	Literature reference giving growth conditions of the host
MIXS:0000252	host_substrate	0..1 String	The growth substrate of the host
MIXS:0000872	host_fam_rel	* String	Relationships to other hosts in the same study; can include multiple relation...
MIXS:0000253	host_infra_spec_name	0..1 String	Taxonomic information about the host below subspecies level
MIXS:0000254	host_infra_spec_rank	0..1 String	Taxonomic rank information about the host below subspecies level, such as var...
MIXS:0000365	host_genotype	0..1 String	Observed genotype
MIXS:0000874	host_phenotype	0..1 String	Phenotype of human or other host
MIXS:0000257	host_dry_mass	0..1 String	Measurement of dry mass
MIXS:0000260	host_color	0..1 String	The color of host
MIXS:0000261	host_shape	0..1 String	Morphological shape of host
MIXS:0000875	gravidity	0..1 String	Whether or not subject is gravid, and if yes date due or date post-conception...
MIXS:0001305	host_number	0..1 String	Number of symbiotic host individuals pooled at the time of collection
MIXS:0001298	host_symbiont	* String	The taxonomic name of the organism(s) found living in mutualistic, commensali...
MIXS:0001308	host_specificity	0..1 recommended HostSpecificityEnum	Level of specificity of symbiont-host interaction: e
MIXS:0001303	symbiont_host_role	0..1 recommended SymbiontHostRoleEnum	Role of the host in the life cycle of the symbiotic organism
MIXS:0001313	host_cellular_loc	0..1 recommended HostCellularLocEnum	The localization of the symbiotic host organism within the host from which it...
MIXS:0001299	association_duration	0..1 String	Time spent in host of the symbiotic organism at the time of sampling; relevan...
MIXS:0001310	host_of_host_coinf	0..1 String	The taxonomic name of any coinfecting organism observed in a symbiotic relati...
MIXS:0001324	host_of_host_name	0..1 String	Common name of the host of the symbiotic host organism
MIXS:0001325	host_of_host_env_loc	* String	For a symbiotic host organism the local anatomical environment within its hos...
MIXS:0001326	host_of_host_env_med	0..1 String	Report the environmental material(s) immediately surrounding the symbiotic ho...
MIXS:0001306	host_of_host_taxid	0..1 String	NCBI taxon id of the host of the symbiotic host organism
MIXS:0001327	host_of_host_sub_id	0..1 String	A unique identifier by which each host of the symbiotic host organism subject...
MIXS:0001319	host_of_host_disease	* String	List of diseases with which the host of the symbiotic host organism has been ...
MIXS:0001328	host_of_host_fam_rel	* String	Familial relationship of the host of the symbiotic host organisms to other ho...
MIXS:0001329	host_of_host_infname	0..1 String	Taxonomic name information of the host of the symbiotic host organism below s...
MIXS:0001330	host_of_host_infrank	0..1 String	Taxonomic rank information about the host of the symbiotic host organism belo...
MIXS:0001331	host_of_host_geno	0..1 String	Observed genotype of the host of the symbiotic host organism
MIXS:0001332	host_of_host_pheno	0..1 String	Phenotype of the host of the symbiotic host organism
MIXS:0001333	host_of_host_gravid	0..1 String	Whether or not the host of the symbiotic host organism is gravid, and if yes ...
MIXS:0001334	host_of_host_totmass	0..1 String	Total mass of the host of the symbiotic host organism at collection, the unit...
MIXS:0000751	chem_administration	* String	List of chemical compounds administered to the host or site where sampling oc...
MIXS:0000754	perturbation	* String	Type of perturbation, e
MIXS:0000183	salinity	0..1 String	The total concentration of all dissolved salts in a liquid or solid sample
MIXS:0000753	oxy_stat_samp	0..1 OxyStatSampEnum	Oxygenation status of sample
MIXS:0000113	temp	0..1 String	Temperature of the sample at the time of sampling
MIXS:0000103	organism_count	* String	Total cell count of any organism (or group of organisms) per gram, volume or ...
MIXS:0000111	samp_vol_we_dna_ext	0..1 String	Volume (ml) or mass (g) of total collected sample processed for DNA extractio...
MIXS:0000110	samp_store_temp	0..1 String	Temperature at which sample was stored, e
MIXS:0000116	samp_store_dur	0..1 String	Duration for which the sample was stored
MIXS:0000755	samp_store_loc	0..1 String	Location at which sample was stored, usually name of a specific freezer/room
MIXS:0001317	samp_store_sol	0..1 String	Solution within which sample was stored, if any
MIXS:0000752	misc_param	* String	Any other measurement performed or parameter collected, that is not listed he...

Aliases

• MIxS-SA (symbiont-associated)

Annotations

• use_cases: the microbiome sequence of a flea sampled from a farm animal

LinkML Source

Direct

name: SymbiontAssociated
annotations:
  use_cases:
    tag: use_cases
    value: the microbiome sequence of a flea sampled from a farm animal
description: A collection of terms appropriate when collecting samples and sequencing
  samples  obtained from an organism that lives in close association with any other
  organism(s).
title: symbiont-associated
from_schema: https://w3id.org/mixs
aliases:
- MIxS-SA (symbiont-associated)
is_a: Extension
slots:
- samp_name
- project_name
- lat_lon
- geo_loc_name
- collection_date
- alt
- depth
- elev
- host_subject_id
- host_common_name
- host_taxid
- source_mat_id
- host_dependence
- type_of_symbiosis
- sym_life_cycle_type
- host_life_stage
- host_age
- urobiom_sex
- mode_transmission
- route_transmission
- host_body_habitat
- host_body_site
- host_body_product
- host_tot_mass
- host_height
- host_length
- host_growth_cond
- host_substrate
- host_fam_rel
- host_infra_spec_name
- host_infra_spec_rank
- host_genotype
- host_phenotype
- host_dry_mass
- host_color
- host_shape
- gravidity
- host_number
- host_symbiont
- host_specificity
- symbiont_host_role
- host_cellular_loc
- association_duration
- host_of_host_coinf
- host_of_host_name
- host_of_host_env_loc
- host_of_host_env_med
- host_of_host_taxid
- host_of_host_sub_id
- host_of_host_disease
- host_of_host_fam_rel
- host_of_host_infname
- host_of_host_infrank
- host_of_host_geno
- host_of_host_pheno
- host_of_host_gravid
- host_of_host_totmass
- chem_administration
- perturbation
- salinity
- oxy_stat_samp
- temp
- organism_count
- samp_vol_we_dna_ext
- samp_store_temp
- samp_store_dur
- samp_store_loc
- samp_store_sol
- misc_param
slot_usage:
  alt:
    name: alt
    recommended: true
  depth:
    name: depth
    examples:
    - value: 10 meter
    recommended: true
  elev:
    name: elev
    recommended: true
  host_body_habitat:
    name: host_body_habitat
    examples:
    - value: anterior end of a tapeworm
  host_body_site:
    name: host_body_site
    examples:
    - value: scolex [UBERON:0015119]
  host_common_name:
    name: host_common_name
    examples:
    - value: trematode
  host_fam_rel:
    name: host_fam_rel
    examples:
    - value: clone;P15
  host_life_stage:
    name: host_life_stage
    examples:
    - value: redia
    required: true
  host_phenotype:
    name: host_phenotype
    examples:
    - value: soldier
  host_subject_id:
    name: host_subject_id
    examples:
    - value: P14
  host_symbiont:
    name: host_symbiont
    examples:
    - value: Paragordius varius
  host_taxid:
    name: host_taxid
    examples:
    - value: '395013'
    string_serialization: '{integer}'
  organism_count:
    name: organism_count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
class_uri: MIXS:0016023

Induced

name: SymbiontAssociated
annotations:
  use_cases:
    tag: use_cases
    value: the microbiome sequence of a flea sampled from a farm animal
description: A collection of terms appropriate when collecting samples and sequencing
  samples  obtained from an organism that lives in close association with any other
  organism(s).
title: symbiont-associated
from_schema: https://w3id.org/mixs
aliases:
- MIxS-SA (symbiont-associated)
is_a: Extension
slot_usage:
  alt:
    name: alt
    recommended: true
  depth:
    name: depth
    examples:
    - value: 10 meter
    recommended: true
  elev:
    name: elev
    recommended: true
  host_body_habitat:
    name: host_body_habitat
    examples:
    - value: anterior end of a tapeworm
  host_body_site:
    name: host_body_site
    examples:
    - value: scolex [UBERON:0015119]
  host_common_name:
    name: host_common_name
    examples:
    - value: trematode
  host_fam_rel:
    name: host_fam_rel
    examples:
    - value: clone;P15
  host_life_stage:
    name: host_life_stage
    examples:
    - value: redia
    required: true
  host_phenotype:
    name: host_phenotype
    examples:
    - value: soldier
  host_subject_id:
    name: host_subject_id
    examples:
    - value: P14
  host_symbiont:
    name: host_symbiont
    examples:
    - value: Paragordius varius
  host_taxid:
    name: host_taxid
    examples:
    - value: '395013'
    string_serialization: '{integer}'
  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: SymbiontAssociated
    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: SymbiontAssociated
    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
  lat_lon:
    name: lat_lon
    description: The geographical origin of the sample as defined by latitude and
      longitude. The values should be reported in decimal degrees, limited to 8 decimal
      points, and in WGS84 system
    title: geographic location (latitude and longitude)
    examples:
    - value: 50.586825 6.408977
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - geographic
    - location
    slot_uri: MIXS:0000009
    alias: lat_lon
    owner: SymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: string
    required: true
    pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$
    structured_pattern:
      syntax: ^{lat} {lon}$
      interpolated: true
      partial_match: true
  geo_loc_name:
    name: geo_loc_name
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name. Country or sea names should be chosen
      from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
      (http://purl.bioontology.org/ontology/GAZ)
    title: geographic location (country and/or sea,region)
    examples:
    - value: 'USA: Maryland, Bethesda'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - geographic
    - location
    slot_uri: MIXS:0000010
    alias: geo_loc_name
    owner: SymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: string
    required: true
    pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
    structured_pattern:
      syntax: '^{text}: {text}, {text}$'
      interpolated: true
      partial_match: true
  collection_date:
    name: collection_date
    description: 'The time of sampling, either as an instance (single point in time)
      or interval. In case no exact time is available, the date/time can be right
      truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
      2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
    title: collection date
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - date
    slot_uri: MIXS:0000011
    alias: collection_date
    owner: SymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: datetime
    required: true
  alt:
    name: alt
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric
      balloons and heights of places such as atmospheric layers and clouds. It is
      used to measure the height of an object which is above the earth's surface.
      In this context, the altitude measurement is the vertical distance between the
      earth's surface above sea level and the sampled position in the air
    title: altitude
    examples:
    - value: 100 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000094
    alias: alt
    owner: SymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - HostAssociated
    - MiscellaneousNaturalOrArtificialEnvironment
    - SymbiontAssociated
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  depth:
    name: depth
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: The vertical distance below local surface. For sediment or soil samples
      depth is measured from sediment or soil surface, respectively. Depth can be
      reported as an interval for subsurface samples
    title: depth
    examples:
    - value: 10 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - depth
    slot_uri: MIXS:0000018
    alias: depth
    owner: SymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  elev:
    name: elev
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit
    title: elevation
    examples:
    - value: 100 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - elevation
    slot_uri: MIXS:0000093
    alias: elev
    owner: SymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - HostAssociated
    - HydrocarbonResourcesCores
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - Water
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  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: P14
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - identifier
    slot_uri: MIXS:0000861
    alias: host_subject_id
    owner: SymbiontAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
  host_common_name:
    name: host_common_name
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ''
    description: Common name of the host
    title: host common name
    examples:
    - value: trematode
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000248
    alias: host_common_name
    owner: SymbiontAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
  host_taxid:
    name: host_taxid
    annotations:
      Expected_value:
        tag: Expected_value
        value: NCBI taxon identifier
    description: NCBI taxon id of the host, e.g. 9606
    title: host taxid
    examples:
    - value: '395013'
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - taxon
    string_serialization: '{integer}'
    slot_uri: MIXS:0000250
    alias: host_taxid
    owner: SymbiontAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
  source_mat_id:
    name: source_mat_id
    annotations:
      Expected_value:
        tag: Expected_value
        value: 'for cultures of microorganisms: identifiers for two culture collections;
          for other material a unique arbitrary identifer'
    description: A unique identifier assigned to a material sample (as defined by
      http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
      digital record of a material sample) used for extracting nucleic acids, and
      subsequent sequencing. The identifier can refer either to the original material
      collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
      /bio_material, or /culture_collection may or may not share the same value as
      the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
      may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
      sampled tissue with the same identifier. However, the /culture_collection qualifier
      may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
      would refer to an identifier from some derived culture from which the nucleic
      acids were extracted (e.g. xatc123 or ark:/2154/R2)
    title: source material identifiers
    examples:
    - value: MPI012345
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - identifier
    - material
    - source
    slot_uri: MIXS:0000026
    alias: source_mat_id
    owner: SymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - SymbiontAssociated
    range: string
    multivalued: true
  host_dependence:
    name: host_dependence
    description: Type of host dependence for the symbiotic host organism to its host
    title: host dependence
    examples:
    - value: obligate
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0001315
    alias: host_dependence
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: HostDependenceEnum
    required: true
  type_of_symbiosis:
    name: type_of_symbiosis
    description: Type of biological interaction established between the symbiotic
      host organism being sampled and its respective host
    title: type of symbiosis
    examples:
    - value: parasitic
    from_schema: https://w3id.org/mixs
    keywords:
    - symbiosis
    - type
    slot_uri: MIXS:0001307
    alias: type_of_symbiosis
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: TypeOfSymbiosisEnum
    recommended: true
  sym_life_cycle_type:
    name: sym_life_cycle_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: type of life cycle of the symbiotic organism (host of the samples)
    description: Type of life cycle of the symbiotic host species (the thing being
      sampled). Simple life cycles occur within a single host, complex ones within
      multiple different hosts over the course of their normal life cycle
    title: symbiotic host organism life cycle type
    examples:
    - value: complex life cycle
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - life
    - organism
    - symbiosis
    - type
    slot_uri: MIXS:0001300
    alias: sym_life_cycle_type
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: SymLifeCycleTypeEnum
    required: true
  host_life_stage:
    name: host_life_stage
    annotations:
      Expected_value:
        tag: Expected_value
        value: stage
    description: Description of life stage of host
    title: host life stage
    examples:
    - value: redia
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - life
    slot_uri: MIXS:0000251
    alias: host_life_stage
    owner: SymbiontAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: true
  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
    from_schema: https://w3id.org/mixs
    keywords:
    - age
    - host
    - host.
    slot_uri: MIXS:0000255
    alias: host_age
    owner: SymbiontAssociated
    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
  urobiom_sex:
    name: urobiom_sex
    annotations:
      Expected_value:
        tag: Expected_value
        value: sex of the symbiotic organism (host of the samples); enumeration
    description: Physical sex of the host
    title: host sex
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000862
    alias: urobiom_sex
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: UrobiomSexEnum
  mode_transmission:
    name: mode_transmission
    description: The process through which the symbiotic host organism entered the
      host from which it was sampled
    title: mode of transmission
    examples:
    - value: horizontal:castrator
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0001312
    alias: mode_transmission
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: ModeTransmissionEnum
    recommended: true
  route_transmission:
    name: route_transmission
    description: Description of path taken by the symbiotic host organism being sampled
      in order to establish a symbiotic relationship with the host (with which it
      was observed at the time of sampling) via a mode of transmission (specified
      in mode_transmission)
    title: route of transmission
    from_schema: https://w3id.org/mixs
    keywords:
    - route
    slot_uri: MIXS:0001316
    alias: route_transmission
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: RouteTransmissionEnum
  host_body_habitat:
    name: host_body_habitat
    description: Original body habitat where the sample was obtained from
    title: host body habitat
    examples:
    - value: anterior end of a tapeworm
    from_schema: https://w3id.org/mixs
    keywords:
    - body
    - habitat
    - host
    - host.
    slot_uri: MIXS:0000866
    alias: host_body_habitat
    owner: SymbiontAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  host_body_site:
    name: host_body_site
    annotations:
      Expected_value:
        tag: Expected_value
        value: FMA or UBERON
    description: Name of body site where the sample was obtained from, such as a specific
      organ or tissue (tongue, lung etc...). Use terms from the foundational model
      of anatomy ontology (fma) or the Uber-anatomy ontology (UBERON)
    title: host body site
    examples:
    - value: scolex [UBERON:0015119]
    from_schema: https://w3id.org/mixs
    keywords:
    - body
    - host
    - site
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000867
    alias: host_body_site
    owner: SymbiontAssociated
    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: SymbiontAssociated
    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
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - mass
    - total
    slot_uri: MIXS:0000263
    alias: host_tot_mass
    owner: SymbiontAssociated
    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
    from_schema: https://w3id.org/mixs
    keywords:
    - height
    - host
    - host.
    slot_uri: MIXS:0000264
    alias: host_height
    owner: SymbiontAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_length:
    name: host_length
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: centimeter, millimeter, meter
    description: The length of subject
    title: host length
    examples:
    - value: 1 meter
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - length
    slot_uri: MIXS:0000256
    alias: host_length
    owner: SymbiontAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_growth_cond:
    name: host_growth_cond
    description: Literature reference giving growth conditions of the host
    title: host growth conditions
    examples:
    - value: https://academic.oup.com/icesjms/article/68/2/349/617247
    from_schema: https://w3id.org/mixs
    keywords:
    - condition
    - growth
    - host
    - host.
    slot_uri: MIXS:0000871
    alias: host_growth_cond
    owner: SymbiontAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: true
  host_substrate:
    name: host_substrate
    description: The growth substrate of the host
    title: host substrate
    examples:
    - value: rock
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000252
    alias: host_substrate
    owner: SymbiontAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  host_fam_rel:
    name: host_fam_rel
    annotations:
      Expected_value:
        tag: Expected_value
        value: relationship type;arbitrary identifier
    description: Relationships to other hosts in the same study; can include multiple
      relationships
    title: host family relationship
    examples:
    - value: clone;P15
    from_schema: https://w3id.org/mixs
    keywords:
    - family
    - host
    - host.
    - relationship
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0000872
    alias: host_fam_rel
    owner: SymbiontAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
    multivalued: true
  host_infra_spec_name:
    name: host_infra_spec_name
    description: Taxonomic information about the host below subspecies level
    title: host infra-specific name
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000253
    alias: host_infra_spec_name
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
  host_infra_spec_rank:
    name: host_infra_spec_rank
    description: Taxonomic rank information about the host below subspecies level,
      such as variety, form, rank etc
    title: host infra-specific rank
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - rank
    slot_uri: MIXS:0000254
    alias: host_infra_spec_rank
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
  host_genotype:
    name: host_genotype
    description: Observed genotype
    title: host genotype
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000365
    alias: host_genotype
    owner: SymbiontAssociated
    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: soldier
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000874
    alias: host_phenotype
    owner: SymbiontAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
  host_dry_mass:
    name: host_dry_mass
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: kilogram, gram
    description: Measurement of dry mass
    title: host dry mass
    examples:
    - value: 500 gram
    from_schema: https://w3id.org/mixs
    keywords:
    - dry
    - host
    - host.
    - mass
    slot_uri: MIXS:0000257
    alias: host_dry_mass
    owner: SymbiontAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_color:
    name: host_color
    description: The color of host
    title: host color
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000260
    alias: host_color
    owner: SymbiontAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  host_shape:
    name: host_shape
    description: Morphological shape of host
    title: host shape
    examples:
    - value: round
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000261
    alias: host_shape
    owner: SymbiontAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  gravidity:
    name: gravidity
    description: Whether or not subject is gravid, and if yes date due or date post-conception,
      specifying which is used
    title: gravidity
    examples:
    - value: yes;due date:2018-05-11
    from_schema: https://w3id.org/mixs
    string_serialization: '{boolean};{timestamp}'
    slot_uri: MIXS:0000875
    alias: gravidity
    owner: SymbiontAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  host_number:
    name: host_number
    annotations:
      Expected_value:
        tag: Expected_value
        value: count
    description: Number of symbiotic host individuals pooled at the time of collection
    title: host number individual
    examples:
    - value: '3'
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - number
    string_serialization: '{float} m'
    slot_uri: MIXS:0001305
    alias: host_number
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
  host_symbiont:
    name: host_symbiont
    annotations:
      Expected_value:
        tag: Expected_value
        value: species name or common name
    description: The taxonomic name of the organism(s) found living in mutualistic,
      commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont
      can have its own symbionts. For example, parasites may have hyperparasites (=parasites
      of the parasite)
    title: observed host symbionts
    examples:
    - value: Paragordius varius
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - observed
    - symbiosis
    slot_uri: MIXS:0001298
    alias: host_symbiont
    owner: SymbiontAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    multivalued: true
  host_specificity:
    name: host_specificity
    description: 'Level of specificity of symbiont-host interaction: e.g. generalist
      (symbiont able to establish associations with distantly related hosts) or species-specific'
    title: host specificity
    examples:
    - value: species-specific
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0001308
    alias: host_specificity
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: HostSpecificityEnum
    recommended: true
  symbiont_host_role:
    name: symbiont_host_role
    description: Role of the host in the life cycle of the symbiotic organism
    title: host of the symbiont role
    examples:
    - value: intermediate
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - symbiosis
    slot_uri: MIXS:0001303
    alias: symbiont_host_role
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: SymbiontHostRoleEnum
    recommended: true
  host_cellular_loc:
    name: host_cellular_loc
    description: 'The localization of the symbiotic host organism within the host
      from which it was sampled: e.g. intracellular if the symbiotic host organism
      is localized within the cells or extracellular if the symbiotic host organism
      is localized outside of cells'
    title: host cellular location
    examples:
    - value: extracellular
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - location
    slot_uri: MIXS:0001313
    alias: host_cellular_loc
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: HostCellularLocEnum
    recommended: true
  association_duration:
    name: association_duration
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: year, day, hour
    description: Time spent in host of the symbiotic organism at the time of sampling;
      relevant scale depends on symbiotic organism and study
    title: duration of association with the host
    from_schema: https://w3id.org/mixs
    keywords:
    - duration
    - host
    - host.
    - period
    slot_uri: MIXS:0001299
    alias: association_duration
    owner: SymbiontAssociated
    domain_of:
    - 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_of_host_coinf:
    name: host_of_host_coinf
    annotations:
      Expected_value:
        tag: Expected_value
        value: species name of coinfecting organism(s)
    description: The taxonomic name of any coinfecting organism observed in a symbiotic
      relationship with the host of the sampled host organism. e.g. where a sample
      collected from a host trematode species (A) which was collected from a host_of_host
      fish (B) that was also infected with a nematode (C), the value here would be
      (C) the nematode {species name} or {common name}. Multiple co-infecting species
      may be added in a comma-separated list. For listing symbiotic organisms associated
      with the host (A) use the term Observed host symbiont
    title: observed coinfecting organisms in host of host
    examples:
    - value: Maritrema novaezealandense
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - observed
    - organism
    slot_uri: MIXS:0001310
    alias: host_of_host_coinf
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
  host_of_host_name:
    name: host_of_host_name
    description: Common name of the host of the symbiotic host organism
    title: host of the symbiotic host common name
    examples:
    - value: snail
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - symbiosis
    slot_uri: MIXS:0001324
    alias: host_of_host_name
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
  host_of_host_env_loc:
    name: host_of_host_env_loc
    annotations:
      Expected_value:
        tag: Expected_value
        value: UBERON term(s), multiple values can be separated by pipes
    description: For a symbiotic host organism the local anatomical environment within
      its host may have causal influences. Report the anatomical entity(s) which are
      in the direct environment of the symbiotic host organism being sampled and which
      you believe have significant causal influences on your sample or specimen. For
      example, if the symbiotic host organism being sampled is an intestinal worm,
      its local environmental context will be the term for intestine from UBERON (http://uberon.github.io/)
    title: host of the symbiotic host local environmental context
    examples:
    - value: small intestine[uberon:0002108]
    from_schema: https://w3id.org/mixs
    keywords:
    - context
    - environmental
    - host
    - host.
    - symbiosis
    string_serialization: small intestine [UBERON:0002108]
    slot_uri: MIXS:0001325
    alias: host_of_host_env_loc
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    multivalued: true
  host_of_host_env_med:
    name: host_of_host_env_med
    annotations:
      Expected_value:
        tag: Expected_value
        value: An ontology term for a material such as a tissue type or excreted substance
    description: 'Report the environmental material(s) immediately surrounding the
      symbiotic host organism at the time of sampling. This usually will be a tissue
      or substance type from the host, but may be another material if the symbiont
      is external to the host. We recommend using classes from the UBERON ontology,
      but subclasses of ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483)
      may also be used. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
      . Terms from other OBO ontologies are permissible as long as they reference
      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
      (e.g. intestines, heart).MIxS . Terms from other OBO ontologies are permissible
      as long as they reference mass/volume nouns (e.g. air, water, blood) and not
      discrete, countable entities (e.g. intestines, heart)'
    title: host of the symbiotic host environemental medium
    examples:
    - value: feces[uberon:0001988]
    from_schema: https://w3id.org/mixs
    keywords:
    - environmental
    - host
    - host.
    - symbiosis
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0001326
    alias: host_of_host_env_med
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
  host_of_host_taxid:
    name: host_of_host_taxid
    annotations:
      Expected_value:
        tag: Expected_value
        value: NCBI taxon identifier of the host of the symbiotic taxon organism
    description: NCBI taxon id of the host of the symbiotic host organism
    title: host of the symbiotic host taxon id
    examples:
    - value: '145637'
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - identifier
    - symbiosis
    - taxon
    string_serialization: '{integer}'
    slot_uri: MIXS:0001306
    alias: host_of_host_taxid
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
  host_of_host_sub_id:
    name: host_of_host_sub_id
    description: 'A unique identifier by which each host of the symbiotic host organism
      subject can be referred to, de-identified, e.g. #H14'
    title: host of the symbiotic host subject id
    examples:
    - value: H3
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - identifier
    - symbiosis
    slot_uri: MIXS:0001327
    alias: host_of_host_sub_id
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
  host_of_host_disease:
    name: host_of_host_disease
    annotations:
      Expected_value:
        tag: Expected_value
        value: disease name or Disease Ontology term
    description: List of diseases with which the host of the symbiotic host organism
      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 of the symbiotic host disease status
    examples:
    - value: rabies [DOID:11260]
    from_schema: https://w3id.org/mixs
    keywords:
    - disease
    - host
    - host.
    - status
    - symbiosis
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0001319
    alias: host_of_host_disease
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    multivalued: true
  host_of_host_fam_rel:
    name: host_of_host_fam_rel
    annotations:
      Expected_value:
        tag: Expected_value
        value: relationship type;arbitrary identifier
    description: Familial relationship of the host of the symbiotic host organisms
      to other hosts of symbiotic host organism in the same study; can include multiple
      relationships
    title: host of the symbiotic host family relationship
    from_schema: https://w3id.org/mixs
    keywords:
    - family
    - host
    - host.
    - relationship
    - symbiosis
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0001328
    alias: host_of_host_fam_rel
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    multivalued: true
  host_of_host_infname:
    name: host_of_host_infname
    description: Taxonomic name information of the host of the symbiotic host organism
      below subspecies level
    title: host of the symbiotic host infra-specific name
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - symbiosis
    slot_uri: MIXS:0001329
    alias: host_of_host_infname
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
  host_of_host_infrank:
    name: host_of_host_infrank
    description: Taxonomic rank information about the host of the symbiotic host organism
      below subspecies level, such as variety, form, rank etc
    title: host of the symbiotic host infra-specific rank
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - rank
    - symbiosis
    slot_uri: MIXS:0001330
    alias: host_of_host_infrank
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
  host_of_host_geno:
    name: host_of_host_geno
    description: Observed genotype of the host of the symbiotic host organism
    title: host of the symbiotic host genotype
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - symbiosis
    slot_uri: MIXS:0001331
    alias: host_of_host_geno
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
  host_of_host_pheno:
    name: host_of_host_pheno
    annotations:
      Expected_value:
        tag: Expected_value
        value: phenotype of the host of the symbiotic organism; PATO
    description: Phenotype of the host of the symbiotic host organism. For phenotypic
      quality ontology (PATO) terms, see http://purl.bioontology.org/ontology/pato
    title: host of the symbiotic host phenotype
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - symbiosis
    string_serialization: '{term}'
    slot_uri: MIXS:0001332
    alias: host_of_host_pheno
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
  host_of_host_gravid:
    name: host_of_host_gravid
    annotations:
      Expected_value:
        tag: Expected_value
        value: gravidity status;timestamp
    description: Whether or not the host of the symbiotic host organism is gravid,
      and if yes date due or date post-conception, specifying which is used
    title: host of the symbiotic host gravidity
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - symbiosis
    string_serialization: '{boolean};{timestamp}'
    slot_uri: MIXS:0001333
    alias: host_of_host_gravid
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
  host_of_host_totmass:
    name: host_of_host_totmass
    description: Total mass of the host of the symbiotic host organism at collection,
      the unit depends on the host
    title: host of the symbiotic host total mass
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - mass
    - symbiosis
    - total
    slot_uri: MIXS:0001334
    alias: host_of_host_totmass
    owner: SymbiontAssociated
    domain_of:
    - 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
  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: SymbiontAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: 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: SymbiontAssociated
    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: SymbiontAssociated
    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: SymbiontAssociated
    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: SymbiontAssociated
    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: SymbiontAssociated
    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: SymbiontAssociated
    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: SymbiontAssociated
    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: SymbiontAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
    structured_pattern:
      syntax: ^{duration}$
      interpolated: true
      partial_match: true
  samp_store_loc:
    name: samp_store_loc
    annotations:
      Expected_value:
        tag: Expected_value
        value: location name
    description: Location at which sample was stored, usually name of a specific freezer/room
    title: sample storage location
    examples:
    - value: Freezer no:5
    from_schema: https://w3id.org/mixs
    keywords:
    - location
    - sample
    - storage
    slot_uri: MIXS:0000755
    alias: samp_store_loc
    owner: SymbiontAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
  samp_store_sol:
    name: samp_store_sol
    annotations:
      Expected_value:
        tag: Expected_value
        value: solution name
    description: Solution within which sample was stored, if any
    title: sample storage solution
    examples:
    - value: 5% ethanol
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - storage
    slot_uri: MIXS:0001317
    alias: samp_store_sol
    owner: SymbiontAssociated
    domain_of:
    - SymbiontAssociated
    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: SymbiontAssociated
    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:0016023