Class: Symbiont-associatedMIMARKSSpecimen

Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package symbiont-associated

URI: MIXS:Symbiont-associatedMIMARKSSpecimen

Inheritance

• Symbiont-associated
  • Symbiont-associatedMIMARKSSpecimen [ MIMARKSSpecimen]

Slots

Name	Cardinality and Range	Description	Inheritance
samp_name	1..1 String	A local identifier or name that for the material sample used for extracting n...	MIMARKSSpecimen
samp_taxon_id	1..1 String	NCBI taxon id of the sample	MIMARKSSpecimen
project_name	1..1 String	Name of the project within which the sequencing was organized	MIMARKSSpecimen
experimental_factor	0..1 recommended String	Experimental factors are essentially the variable aspects of an experiment de...	MIMARKSSpecimen
lat_lon	1..1 String	The geographical origin of the sample as defined by latitude and longitude	MIMARKSSpecimen, Symbiont-associated
geo_loc_name	1..1 String	The geographical origin of the sample as defined by the country or sea name f...	MIMARKSSpecimen, Symbiont-associated
collection_date	1..1 Date	The time of sampling, either as an instance (single point in time) or interva...	MIMARKSSpecimen, Symbiont-associated
neg_cont_type	0..1 recommended NegContTypeEnum	The substance or equipment used as a negative control in an investigation	MIMARKSSpecimen
pos_cont_type	0..1 recommended String	The substance, mixture, product, or apparatus used to verify that a process w...	MIMARKSSpecimen
env_broad_scale	1..1 String	Report the major environmental system the sample or specimen came from	MIMARKSSpecimen, Symbiont-associated
env_local_scale	1..1 String	Report the entity or entities which are in the sample or specimen’s local vic...	MIMARKSSpecimen, Symbiont-associated
env_medium	1..1 String	Report the environmental material(s) immediately surrounding the sample or sp...	MIMARKSSpecimen, Symbiont-associated
source_mat_id	0..1 recommended String	A unique identifier assigned to a material sample (as defined by http://rs	MIMARKSSpecimen
rel_to_oxygen	0..1 RelToOxygenEnum	Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ...	MIMARKSSpecimen
samp_collec_device	0..1 recommended String	The device used to collect an environmental sample	MIMARKSSpecimen
samp_collec_method	0..1 recommended String	The method employed for collecting the sample	MIMARKSSpecimen
samp_mat_process	0..1 recommended String	A brief description of any processing applied to the sample during or after r...	MIMARKSSpecimen
size_frac	0..1 String	Filtering pore size used in sample preparation	MIMARKSSpecimen
samp_size	0..1 recommended QuantityValue	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...	MIMARKSSpecimen
samp_vol_we_dna_ext	0..1 QuantityValue	Volume (ml) or mass (g) of total collected sample processed for DNA extractio...	MIMARKSSpecimen
nucl_acid_ext	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...	MIMARKSSpecimen
nucl_acid_amp	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...	MIMARKSSpecimen
lib_size	0..1 recommended Integer	Total number of clones in the library prepared for the project	MIMARKSSpecimen
lib_reads_seqd	0..1 recommended Integer	Total number of clones sequenced from the library	MIMARKSSpecimen
lib_layout	0..1 recommended LibLayoutEnum	Specify whether to expect single, paired, or other configuration of reads	MIMARKSSpecimen
lib_vector	0..1 recommended String	Cloning vector type(s) used in construction of libraries	MIMARKSSpecimen
lib_screen	0..1 recommended String	Specific enrichment or screening methods applied before and/or after creating...	MIMARKSSpecimen
target_gene	1..1 String	Targeted gene or locus name for marker gene studies	MIMARKSSpecimen
target_subfragment	0..1 recommended String	Name of subfragment of a gene or locus	MIMARKSSpecimen
pcr_primers	0..1 recommended String	PCR primers that were used to amplify the sequence of the targeted gene, locu...	MIMARKSSpecimen
mid	0..1 recommended String	Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe...	MIMARKSSpecimen
adapters	0..1 recommended String	Adapters provide priming sequences for both amplification and sequencing of t...	MIMARKSSpecimen
pcr_cond	0..1 recommended String	Description of reaction conditions and components of PCR in the form of 'init...	MIMARKSSpecimen
seq_meth	1..1 String	Sequencing machine used	MIMARKSSpecimen
seq_quality_check	0..1 recommended String	Indicate if the sequence has been called by automatic systems (none) or under...	MIMARKSSpecimen
chimera_check	0..1 recommended String	Tool(s) used for chimera checking, including version number and parameters, t...	MIMARKSSpecimen
assembly_software	0..1 recommended String	Tool(s) used for assembly, including version number and parameters	MIMARKSSpecimen
associated_resource	0..1 recommended String	A related resource that is referenced, cited, or otherwise associated to the ...	MIMARKSSpecimen
sop	0..1 recommended String	Standard operating procedures used in assembly and/or annotation of genomes, ...	MIMARKSSpecimen
depth	0..1 QuantityValue	The vertical distance below local surface, e	Symbiont-associated
alt	0..1 QuantityValue	Altitude is a term used to identify heights of objects such as airplanes, spa...	Symbiont-associated
elev	0..1 QuantityValue	Elevation of the sampling site is its height above a fixed reference point, m...	Symbiont-associated
temp	0..1 QuantityValue	Temperature of the sample at the time of sampling	Symbiont-associated
sample_name	1..1 String	Sample Name is a name that you choose for the sample	Symbiont-associated
host_subject_id	0..1 String	A unique identifier by which each subject can be referred to, de-identified	Symbiont-associated
host_common_name	0..1 String	Common name of the host	Symbiont-associated
host_taxid	0..1 String	NCBI taxon id of the host, e	Symbiont-associated
host_dependence	1..1 String	Type of host dependence for the symbiotic host organism to its host	Symbiont-associated
type_of_symbiosis	0..1 TypeOfSymbiosisEnum	Type of biological interaction established between the symbiotic host organis...	Symbiont-associated
sym_life_cycle_type	1..1 String	Type of life cycle of the symbiotic host species (the thing being sampled)	Symbiont-associated
host_life_stage	1..1 String	Description of life stage of host	Symbiont-associated
host_age	0..1 QuantityValue	Age of host at the time of sampling; relevant scale depends on species and st...	Symbiont-associated
host_sex	0..1 HostSexEnum	Gender or physical sex of the host	Symbiont-associated
mode_transmission	0..1 ModeTransmissionEnum	The process through which the symbiotic host organism entered the host from w...	Symbiont-associated
route_transmission	0..1 RouteTransmissionEnum	Description of path taken by the symbiotic host organism being sampled in ord...	Symbiont-associated
host_body_habitat	0..1 String	Original body habitat where the sample was obtained from	Symbiont-associated
host_body_site	0..1 String	Name of body site where the sample was obtained from, such as a specific orga...	Symbiont-associated
host_body_product	0..1 String	Substance produced by the body, e	Symbiont-associated
host_tot_mass	0..1 QuantityValue	Total mass of the host at collection, the unit depends on host	Symbiont-associated
host_height	0..1 QuantityValue	The height of subject	Symbiont-associated
host_length	0..1 QuantityValue	The length of subject	Symbiont-associated
host_growth_cond	0..1 String	Literature reference giving growth conditions of the host	Symbiont-associated
host_substrate	0..1 String	The growth substrate of the host	Symbiont-associated
host_family_relationship	0..1 String	Relationships to other hosts in the same study; can include multiple relation...	Symbiont-associated
host_infra_specific_name	0..1 String	Taxonomic information about the host below subspecies level	Symbiont-associated
host_infra_specific_rank	0..1 String	Taxonomic rank information about the host below subspecies level, such as var...	Symbiont-associated
host_genotype	0..1 String	Observed genotype	Symbiont-associated
host_phenotype	0..1 String	Phenotype of human or other host	Symbiont-associated
host_dry_mass	0..1 QuantityValue	Measurement of dry mass	Symbiont-associated
host_color	0..1 String	The color of host	Symbiont-associated
host_shape	0..1 String	Morphological shape of host	Symbiont-associated
gravidity	0..1 String	Whether or not subject is gravid, and if yes date due or date post-conception...	Symbiont-associated
host_number	0..1 String	Number of symbiotic host individuals pooled at the time of collection	Symbiont-associated
host_symbiont	0..* String	The taxonomic name of the organism(s) found living in mutualistic, commensali...	Symbiont-associated
host_specificity	0..1 HostSpecificityEnum	Level of specificity of symbiont-host interaction: e	Symbiont-associated
symbiont_host_role	0..1 SymbiontHostRoleEnum	Role of the host in the life cycle of the symbiotic organism	Symbiont-associated
host_cellular_loc	0..1 HostCellularLocEnum	The localization of the symbiotic host organism within the host from which it...	Symbiont-associated
association_duration	0..1 QuantityValue	Time spent in host of the symbiotic organism at the time of sampling; relevan...	Symbiont-associated
host_of_host_coinf	0..1 String	The taxonomic name of any coinfecting organism observed in a symbiotic relati...	Symbiont-associated
host_of_host_name	0..1 String	Common name of the host of the symbiotic host organism	Symbiont-associated
host_of_host_env_loc	0..* String	For a symbiotic host organism the local anatomical environment within its hos...	Symbiont-associated
host_of_host_env_med	0..1 String	Report the environmental material(s) immediately surrounding the symbiotic ho...	Symbiont-associated
host_of_host_taxid	0..1 Integer	NCBI taxon id of the host of the symbiotic host organism	Symbiont-associated
host_of_host_sub_id	0..1 String	A unique identifier by which each host of the symbiotic host organism subject...	Symbiont-associated
host_of_host_disease	0..* String	List of diseases with which the host of the symbiotic host organism has been ...	Symbiont-associated
host_of_host_fam_rel	0..* String	Familial relationship of the host of the symbiotic host organisms to other ho...	Symbiont-associated
host_of_host_infname	0..1 String	Taxonomic name information of the host of the symbiotic host organism below s...	Symbiont-associated
host_of_host_infrank	0..1 String	Taxonomic rank information about the host of the symbiotic host organism belo...	Symbiont-associated
host_of_host_geno	0..1 String	Observed genotype of the host of the symbiotic host organism	Symbiont-associated
host_of_host_pheno	0..1 String	Phenotype of the host of the symbiotic host organism	Symbiont-associated
host_of_host_gravid	0..1 String	Whether or not the host of the symbiotic host organism is gravid, and if yes ...	Symbiont-associated
host_of_host_totmass	0..1 QuantityValue	Total mass of the host of the symbiotic host organism at collection, the unit...	Symbiont-associated
chem_administration	0..* String	List of chemical compounds administered to the host or site where sampling oc...	Symbiont-associated
perturbation	0..* String	Type of perturbation, e	Symbiont-associated
samp_salinity	0..1 QuantityValue	Salinity is the total concentration of all dissolved salts in a liquid or sol...	Symbiont-associated
oxy_stat_samp	0..1 OxyStatSampEnum	Oxygenation status of sample	Symbiont-associated
organism_count	0..* OrganismCountEnum	Total cell count of any organism (or group of organisms) per gram, volume or ...	Symbiont-associated
samp_store_temp	0..1 QuantityValue	Temperature at which sample was stored, e	Symbiont-associated
samp_store_dur	0..1 String	Duration for which the sample was stored	Symbiont-associated
samp_store_loc	0..1 String	Location at which sample was stored, usually name of a specific freezer/room	Symbiont-associated
samp_store_sol	0..1 String	Solution within which sample was stored, if any	Symbiont-associated
misc_param	0..* String	Any other measurement performed or parameter collected, that is not listed he...	Symbiont-associated

Identifier and Mapping Information

Schema Source

• from schema: http://w3id.org/mixs

Mappings

Mapping Type	Mapped Value
self	MIXS:Symbiont-associatedMIMARKSSpecimen
native	MIXS:Symbiont-associatedMIMARKSSpecimen

LinkML Source

Direct

name: symbiont-associated MIMARKS specimen
description: 'Combinatorial checklist Minimal Information about a Marker Specimen:
  specimen with environmental package symbiont-associated'
from_schema: http://w3id.org/mixs
is_a: symbiont-associated
mixins:
- MIMARKS specimen

Induced

name: symbiont-associated MIMARKS specimen
description: 'Combinatorial checklist Minimal Information about a Marker Specimen:
  specimen with environmental package symbiont-associated'
from_schema: http://w3id.org/mixs
is_a: symbiont-associated
mixins:
- MIMARKS specimen
attributes:
  samp_name:
    name: samp_name
    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
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{text}'
    slot_uri: MIXS:0001107
    multivalued: false
    alias: samp_name
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
  samp_taxon_id:
    name: samp_taxon_id
    description: NCBI taxon id of the sample.  Maybe be a single taxon or mixed taxa
      sample. Use 'synthetic metagenome’ for mock community/positive controls, or
      'blank sample' for negative controls.
    title: Taxonomy ID of DNA sample
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{text} [NCBI:txid]'
    slot_uri: MIXS:0001320
    multivalued: false
    alias: samp_taxon_id
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
  project_name:
    name: project_name
    description: Name of the project within which the sequencing was organized
    title: project name
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{text}'
    slot_uri: MIXS:0000092
    multivalued: false
    alias: project_name
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
  experimental_factor:
    name: experimental_factor
    description: Experimental factors are essentially the variable aspects of an experiment
      design which can be used to describe an experiment, or set of experiments, in
      an increasingly detailed manner. This field accepts ontology terms from Experimental
      Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For
      a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;
      for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
    title: experimental factor
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000008
    multivalued: false
    alias: experimental_factor
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: 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 and in WGS84 system
    title: geographic location (latitude and longitude)
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{float} {float}'
    slot_uri: MIXS:0000009
    multivalued: false
    alias: lat_lon
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: 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)
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{term}: {term}, {text}'
    slot_uri: MIXS:0000010
    multivalued: false
    alias: geo_loc_name
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: 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
    from_schema: http://w3id.org/mixs
    is_a: environment field
    slot_uri: MIXS:0000011
    multivalued: false
    alias: collection_date
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: date
    required: true
  neg_cont_type:
    name: neg_cont_type
    description: The substance or equipment used as a negative control in an investigation
    title: negative control type
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    slot_uri: MIXS:0001321
    multivalued: false
    alias: neg_cont_type
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: neg_cont_type_enum
    recommended: true
  pos_cont_type:
    name: pos_cont_type
    description: The substance, mixture, product, or apparatus used to verify that
      a process which is part of an investigation delivers a true positive.
    title: positive control type
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    multivalued: false
    alias: pos_cont_type
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  env_broad_scale:
    name: env_broad_scale
    description: 'Report the major environmental system the sample or specimen came
      from. The system(s) identified should have a coarse spatial grain, to provide
      the general environmental context of where the sampling was done (e.g. in the
      desert or a rainforest). We recommend using subclasses of EnvO’s biome class:  http://purl.obolibrary.org/obo/ENVO_00000428.
      EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: broad-scale environmental context
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    multivalued: false
    alias: env_broad_scale
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  env_local_scale:
    name: env_local_scale
    description: 'Report the entity or entities which are in the sample or specimen’s
      local vicinity and which you believe have significant causal influences on your
      sample or specimen. We recommend using EnvO terms which are of smaller spatial
      grain than your entry for env_broad_scale. Terms, such as anatomical sites,
      from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON)
      are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'
    title: local environmental context
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000013
    multivalued: false
    alias: env_local_scale
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  env_medium:
    name: env_medium
    description: 'Report the environmental material(s) immediately surrounding the
      sample or specimen at the time of sampling. We recommend using subclasses of
      ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
      documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
      . Terms from other OBO ontologies are permissible as long as they reference
      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
      (e.g. a tree, a leaf, a table top).'
    title: environmental medium
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000014
    multivalued: false
    alias: env_medium
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  source_mat_id:
    name: source_mat_id
    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
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{text}'
    slot_uri: MIXS:0000026
    multivalued: false
    alias: source_mat_id
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
    recommended: true
  rel_to_oxygen:
    name: rel_to_oxygen
    description: Is this organism an aerobe, anaerobe? Please note that aerobic and
      anaerobic are valid descriptors for microbial environments
    title: relationship to oxygen
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000015
    multivalued: false
    alias: rel_to_oxygen
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS bacteria
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    range: rel_to_oxygen_enum
    required: false
  samp_collec_device:
    name: samp_collec_device
    description: The device used to collect an environmental sample. This field accepts
      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
    title: sample collection device
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000002
    multivalued: false
    alias: samp_collec_device
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  samp_collec_method:
    name: samp_collec_method
    description: The method employed for collecting the sample.
    title: sample collection method
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001225
    multivalued: false
    alias: samp_collec_method
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  samp_mat_process:
    name: samp_mat_process
    description: A brief description of any processing applied to the sample during
      or after retrieving the sample from environment, or a link to the relevant protocol(s)
      performed.
    title: sample material processing
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{text}'
    slot_uri: MIXS:0000016
    multivalued: false
    alias: samp_mat_process
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  size_frac:
    name: size_frac
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    multivalued: false
    alias: size_frac
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  samp_size:
    name: samp_size
    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
      sample collected.
    title: amount or size of sample collected
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000001
    multivalued: false
    alias: samp_size
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: quantity value
    recommended: true
  samp_vol_we_dna_ext:
    name: samp_vol_we_dna_ext
    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
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000111
    multivalued: false
    alias: samp_vol_we_dna_ext
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: quantity value
    required: false
  nucl_acid_ext:
    name: nucl_acid_ext
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the material separation to recover
      the nucleic acid fraction from a sample
    title: nucleic acid extraction
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000037
    multivalued: false
    alias: nucl_acid_ext
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  nucl_acid_amp:
    name: nucl_acid_amp
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the enzymatic amplification (PCR,
      TMA, NASBA) of specific nucleic acids
    title: nucleic acid amplification
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000038
    multivalued: false
    alias: nucl_acid_amp
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  lib_size:
    name: lib_size
    description: Total number of clones in the library prepared for the project
    title: library size
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000039
    multivalued: false
    alias: lib_size
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: integer
    recommended: true
  lib_reads_seqd:
    name: lib_reads_seqd
    description: Total number of clones sequenced from the library
    title: library reads sequenced
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000040
    multivalued: false
    alias: lib_reads_seqd
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: integer
    recommended: true
  lib_layout:
    name: lib_layout
    description: Specify whether to expect single, paired, or other configuration
      of reads
    title: library layout
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000041
    multivalued: false
    alias: lib_layout
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: lib_layout_enum
    recommended: true
  lib_vector:
    name: lib_vector
    description: Cloning vector type(s) used in construction of libraries
    title: library vector
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000042
    multivalued: false
    alias: lib_vector
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  lib_screen:
    name: lib_screen
    description: Specific enrichment or screening methods applied before and/or after
      creating libraries
    title: library screening strategy
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000043
    multivalued: false
    alias: lib_screen
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  target_gene:
    name: target_gene
    description: Targeted gene or locus name for marker gene studies
    title: target gene
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000044
    multivalued: false
    alias: target_gene
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    required: true
  target_subfragment:
    name: target_subfragment
    description: Name of subfragment of a gene or locus. Important to e.g. identify
      special regions on marker genes like V6 on 16S rRNA
    title: target subfragment
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000045
    multivalued: false
    alias: target_subfragment
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    recommended: true
  pcr_primers:
    name: pcr_primers
    description: PCR primers that were used to amplify the sequence of the targeted
      gene, locus or subfragment. This field should contain all the primers used for
      a single PCR reaction if multiple forward or reverse primers are present in
      a single PCR reaction. The primer sequence should be reported in uppercase letters
    title: pcr primers
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: FWD:{dna};REV:{dna}
    slot_uri: MIXS:0000046
    multivalued: false
    alias: pcr_primers
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    recommended: true
  mid:
    name: mid
    description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
      used to specifically tag unique samples in a sequencing run. Sequence should
      be reported in uppercase letters
    title: multiplex identifiers
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{dna}'
    slot_uri: MIXS:0000047
    multivalued: false
    alias: mid
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  adapters:
    name: adapters
    description: Adapters provide priming sequences for both amplification and sequencing
      of the sample-library fragments. Both adapters should be reported; in uppercase
      letters
    title: adapters
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{dna};{dna}'
    slot_uri: MIXS:0000048
    multivalued: false
    alias: adapters
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  pcr_cond:
    name: pcr_cond
    description: Description of reaction conditions and components of PCR in the form
      of 'initial denaturation:94degC_1.5min; annealing=...'
    title: pcr conditions
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
      elongation:degrees_minutes;total cycles
    slot_uri: MIXS:0000049
    multivalued: false
    alias: pcr_cond
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    recommended: true
  seq_meth:
    name: seq_meth
    description: Sequencing machine used. Where possible the term should be taken
      from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).
    title: sequencing method
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000050
    multivalued: false
    alias: seq_meth
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
  seq_quality_check:
    name: seq_quality_check
    description: Indicate if the sequence has been called by automatic systems (none)
      or undergone a manual editing procedure (e.g. by inspecting the raw data or
      chromatograms). Applied only for sequences that are not submitted to SRA,ENA
      or DRA
    title: sequence quality check
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '[none|manually edited]'
    slot_uri: MIXS:0000051
    multivalued: false
    alias: seq_quality_check
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    recommended: true
  chimera_check:
    name: chimera_check
    description: Tool(s) used for chimera checking, including version number and parameters,
      to discover and remove chimeric sequences. A chimeric sequence is comprised
      of two or more phylogenetically distinct parent sequences.
    title: chimera check software
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{software};{version};{parameters}'
    slot_uri: MIXS:0000052
    multivalued: false
    alias: chimera_check
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    recommended: true
  assembly_software:
    name: assembly_software
    description: Tool(s) used for assembly, including version number and parameters
    title: assembly software
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{software};{version};{parameters}'
    slot_uri: MIXS:0000058
    multivalued: false
    alias: assembly_software
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  associated resource:
    name: associated resource
    description: A related resource that is referenced, cited, or otherwise associated
      to the sequence.
    title: relevant electronic resources
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID} | {DOI} | {URL}'
    slot_uri: MIXS:0000091
    multivalued: false
    alias: associated_resource
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  sop:
    name: sop
    description: Standard operating procedures used in assembly and/or annotation
      of genomes, metagenomes or environmental sequences
    title: relevant standard operating procedures
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000090
    multivalued: false
    alias: sop
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  depth:
    name: depth
    description: The vertical distance below local surface, e.g. for sediment or soil
      samples depth is measured from sediment or soil surface, respectively. Depth
      can be reported as an interval for subsurface samples.
    title: depth
    from_schema: http://w3id.org/mixs
    is_a: environment field
    slot_uri: MIXS:0000018
    multivalued: false
    alias: depth
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
    required: false
  alt:
    name: alt
    description: Altitude is a term used to identify heights of objects such as airplanes,
      space shuttles, rockets, atmospheric balloons and heights of places such as
      atmospheric layers and clouds. It is used to measure the height of an object
      which is above the earth's surface. In this context, the altitude measurement
      is the vertical distance between the earth's surface above sea level and the
      sampled position in the air
    title: altitude
    from_schema: http://w3id.org/mixs
    is_a: environment field
    slot_uri: MIXS:0000094
    multivalued: false
    alias: alt
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
    required: false
  elev:
    name: elev
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit.
    title: elevation
    from_schema: http://w3id.org/mixs
    is_a: environment field
    slot_uri: MIXS:0000093
    multivalued: false
    alias: elev
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
    required: false
  temp:
    name: temp
    description: Temperature of the sample at the time of sampling.
    title: temperature
    from_schema: http://w3id.org/mixs
    is_a: environment field
    slot_uri: MIXS:0000113
    multivalued: false
    alias: temp
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
    required: false
  sample_name:
    name: sample_name
    description: Sample Name is a name that you choose for the sample. It can have
      any format, but we suggest that you make it concise, unique and consistent within
      your lab, and as informative as possible. Every Sample Name from a single Submitter
      must be unique.
    title: sample name
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001107
    multivalued: false
    alias: sample_name
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000861
    multivalued: false
    alias: host_subject_id
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    range: string
    required: false
  host_common_name:
    name: host_common_name
    description: Common name of the host.
    title: host common name
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000248
    multivalued: false
    alias: host_common_name
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - host-associated
    - agriculture
    range: string
    required: false
  host_taxid:
    name: host_taxid
    description: NCBI taxon id of the host, e.g. 9606
    title: host taxid
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{NCBI taxid}'
    slot_uri: MIXS:0000250
    multivalued: false
    alias: host_taxid
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: string
    required: false
  host_dependence:
    name: host_dependence
    description: Type of host dependence for the symbiotic host organism to its host.
    title: host dependence
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '[facultative|obligate]'
    slot_uri: MIXS:0001315
    multivalued: false
    alias: host_dependence
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001307
    multivalued: false
    alias: type_of_symbiosis
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: type_of_symbiosis_enum
    required: false
  sym_life_cycle_type:
    name: sym_life_cycle_type
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '[complex life cycle | simple life cycle]'
    slot_uri: MIXS:0001300
    multivalued: false
    alias: sym_life_cycle_type
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: true
  host_life_stage:
    name: host_life_stage
    description: Description of life stage of host
    title: host life stage
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000251
    multivalued: false
    alias: host_life_stage
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - host-associated
    - agriculture
    range: string
    required: true
  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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000255
    multivalued: false
    alias: host_age
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  host_sex:
    name: host_sex
    description: Gender or physical sex of the host.
    title: host sex
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000811
    multivalued: false
    alias: host_sex
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    range: host_sex_enum
    required: false
  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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001312
    multivalued: false
    alias: mode_transmission
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: mode_transmission_enum
    required: false
  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: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001316
    multivalued: false
    alias: route_transmission
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: route_transmission_enum
    required: false
  host_body_habitat:
    name: host_body_habitat
    description: Original body habitat where the sample was obtained from
    title: host body habitat
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000866
    multivalued: false
    alias: host_body_habitat
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - host-associated
    range: string
    required: false
  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...). For foundational model of anatomy ontology
      (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,
      please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON
    title: host body site
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000867
    multivalued: false
    alias: host_body_site
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    range: string
    required: false
  host_body_product:
    name: host_body_product
    description: Substance produced by the body, e.g. Stool, mucus, where the sample
      was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy
      ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma
      or https://www.ebi.ac.uk/ols/ontologies/uberon
    title: host body product
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000888
    multivalued: false
    alias: host_body_product
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    range: string
    required: false
  host_tot_mass:
    name: host_tot_mass
    description: Total mass of the host at collection, the unit depends on host
    title: host total mass
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000263
    multivalued: false
    alias: host_tot_mass
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  host_height:
    name: host_height
    description: The height of subject
    title: host height
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000264
    multivalued: false
    alias: host_height
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  host_length:
    name: host_length
    description: The length of subject
    title: host length
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000256
    multivalued: false
    alias: host_length
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  host_growth_cond:
    name: host_growth_cond
    description: Literature reference giving growth conditions of the host
    title: host growth conditions
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0000871
    multivalued: false
    alias: host_growth_cond
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - host-associated
    range: string
    required: false
  host_substrate:
    name: host_substrate
    description: The growth substrate of the host.
    title: host substrate
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000252
    multivalued: false
    alias: host_substrate
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - host-associated
    range: string
    required: false
  host_family_relationship:
    name: host_family_relationship
    description: Relationships to other hosts in the same study; can include multiple
      relationships.
    title: host family relationship
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0000872
    multivalued: false
    alias: host_family_relationship
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  host_infra_specific_name:
    name: host_infra_specific_name
    description: Taxonomic information about the host below subspecies level.
    title: host infra-specific name
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000253
    multivalued: false
    alias: host_infra_specific_name
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  host_infra_specific_rank:
    name: host_infra_specific_rank
    description: Taxonomic rank information about the host below subspecies level,
      such as variety, form, rank etc.
    title: host infra-specific rank
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000254
    multivalued: false
    alias: host_infra_specific_rank
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  host_genotype:
    name: host_genotype
    description: Observed genotype
    title: host genotype
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000365
    multivalued: false
    alias: host_genotype
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: string
    required: false
  host_phenotype:
    name: host_phenotype
    description: Phenotype of human or other host. For phenotypic quality ontology
      (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato.
      For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP
    title: host phenotype
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000874
    multivalued: false
    alias: host_phenotype
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: string
    required: false
  host_dry_mass:
    name: host_dry_mass
    description: Measurement of dry mass
    title: host dry mass
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000257
    multivalued: false
    alias: host_dry_mass
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  host_color:
    name: host_color
    description: The color of host
    title: host color
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000260
    multivalued: false
    alias: host_color
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - host-associated
    range: string
    required: false
  host_shape:
    name: host_shape
    description: Morphological shape of host
    title: host shape
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000261
    multivalued: false
    alias: host_shape
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - host-associated
    range: string
    required: false
  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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{boolean};{timestamp}'
    slot_uri: MIXS:0000875
    multivalued: false
    alias: gravidity
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - host-associated
    range: string
    required: false
  host_number:
    name: host_number
    description: Number of symbiotic host individuals pooled at the time of collection.
    title: host number individual
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{float} m'
    slot_uri: MIXS:0001305
    multivalued: false
    alias: host_number
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  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.
    title: observed host symbionts
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001298
    multivalued: true
    alias: host_symbiont
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - agriculture
    range: string
    required: false
  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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001308
    multivalued: false
    alias: host_specificity
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: host_specificity_enum
    required: false
  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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001303
    multivalued: false
    alias: symbiont_host_role
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: symbiont_host_role_enum
    required: false
  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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001313
    multivalued: false
    alias: host_cellular_loc
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: host_cellular_loc_enum
    required: false
  association_duration:
    name: association_duration
    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: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001299
    multivalued: false
    alias: association_duration
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: quantity value
    required: false
  host_of_host_coinf:
    name: host_of_host_coinf
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001310
    multivalued: false
    alias: host_of_host_coinf
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001324
    multivalued: false
    alias: host_of_host_name
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  host_of_host_env_loc:
    name: host_of_host_env_loc
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001325
    multivalued: true
    alias: host_of_host_env_loc
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  host_of_host_env_med:
    name: host_of_host_env_med
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001326
    multivalued: false
    alias: host_of_host_env_med
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  host_of_host_taxid:
    name: host_of_host_taxid
    description: NCBI taxon id of the host of the symbiotic host organism.
    title: host of the symbiotic host taxon id
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001306
    multivalued: false
    alias: host_of_host_taxid
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: integer
    required: false
  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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001327
    multivalued: false
    alias: host_of_host_sub_id
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  host_of_host_disease:
    name: host_of_host_disease
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0001319
    multivalued: true
    alias: host_of_host_disease
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  host_of_host_fam_rel:
    name: host_of_host_fam_rel
    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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0001328
    multivalued: true
    alias: host_of_host_fam_rel
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001329
    multivalued: false
    alias: host_of_host_infname
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001330
    multivalued: false
    alias: host_of_host_infrank
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001331
    multivalued: false
    alias: host_of_host_geno
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  host_of_host_pheno:
    name: host_of_host_pheno
    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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{term}'
    slot_uri: MIXS:0001332
    multivalued: false
    alias: host_of_host_pheno
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  host_of_host_gravid:
    name: host_of_host_gravid
    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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{boolean};{timestamp}'
    slot_uri: MIXS:0001333
    multivalued: false
    alias: host_of_host_gravid
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001334
    multivalued: false
    alias: host_of_host_totmass
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: quantity value
    required: false
  chem_administration:
    name: chem_administration
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]};{timestamp}'
    slot_uri: MIXS:0000751
    multivalued: true
    alias: chem_administration
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - air
    - agriculture
    range: string
    required: false
  perturbation:
    name: perturbation
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000754
    multivalued: true
    alias: perturbation
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-farm environment
    - food-animal and animal feed
    - air
    - agriculture
    range: string
    required: false
  samp_salinity:
    name: samp_salinity
    description: Salinity is the total concentration of all dissolved salts in a liquid
      or solid (in the form of an extract obtained by centrifugation) 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: sample salinity
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000109
    multivalued: false
    alias: samp_salinity
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    - human-vaginal
    range: quantity value
    required: false
  oxy_stat_samp:
    name: oxy_stat_samp
    description: Oxygenation status of sample
    title: oxygenation status of sample
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000753
    multivalued: false
    alias: oxy_stat_samp
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - air
    - agriculture
    range: oxy_stat_samp_enum
    required: false
  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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000103
    multivalued: true
    alias: organism_count
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - built environment
    - air
    - agriculture
    range: organism_count_enum
    required: false
  samp_store_temp:
    name: samp_store_temp
    description: Temperature at which sample was stored, e.g. -80 degree Celsius
    title: sample storage temperature
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000110
    multivalued: false
    alias: samp_store_temp
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - air
    range: quantity value
    required: false
  samp_store_dur:
    name: samp_store_dur
    description: Duration for which the sample was stored
    title: sample storage duration
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{duration}'
    slot_uri: MIXS:0000116
    multivalued: false
    alias: samp_store_dur
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - air
    - agriculture
    range: string
    required: false
  samp_store_loc:
    name: samp_store_loc
    description: Location at which sample was stored, usually name of a specific freezer/room
    title: sample storage location
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000755
    multivalued: false
    alias: samp_store_loc
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - air
    - agriculture
    range: string
    required: false
  samp_store_sol:
    name: samp_store_sol
    description: Solution within which sample was stored, if any.
    title: sample storage solution
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001317
    multivalued: false
    alias: samp_store_sol
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - symbiont-associated
    range: string
    required: false
  misc_param:
    name: misc_param
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    multivalued: true
    alias: misc_param
    owner: symbiont-associated MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - air
    - agriculture
    range: string
    required: false