Skip to content

Combination: MimarksCSymbiontAssociated

MIxS data that complies with the MimarksC checklist and the SymbiontAssociated Extension

Inheritance

Terms

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... MimarksC, SymbiontAssociated
pcr_primers 0..1 recommended
String		 PCR primers that were used to amplify the sequence of the targeted gene, locu... MimarksC
nucl_acid_amp 0..1 recommended
String		 A link to a literature reference, electronic resource or a standard operating... MimarksC
target_subfragment 0..1 recommended
String		 Name of subfragment of a gene or locus MimarksC
temp 0..1 recommended
String		 Temperature of the sample at the time of sampling MimarksC, SymbiontAssociated
pcr_cond 0..1 recommended
String		 Description of reaction conditions and components of PCR in the form of 'init... MimarksC
nucl_acid_ext 0..1 recommended
String		 A link to a literature reference, electronic resource or a standard operating... MimarksC
samp_size 0..1
String		 The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... MimarksC
isol_growth_condt 1..1
String		 Publication reference in the form of pubmed ID (pmid), digital object identif... MimarksC
alt 0..1 recommended
String		 Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... MimarksC, SymbiontAssociated
source_mat_id 0..* recommended
String		 A unique identifier assigned to a material sample (as defined by http://rs MimarksC, SymbiontAssociated
extrachrom_elements 0..1
Integer		 Do plasmids exist of significant phenotypic consequence (e MimarksC
samp_vol_we_dna_ext 0..1
String		 Volume (ml) or mass (g) of total collected sample processed for DNA extractio... MimarksC, SymbiontAssociated
rel_to_oxygen 0..1 recommended
RELTOOXYGENENUM		 Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ... MimarksC
samp_collect_device 0..1
String		 The device used to collect an environmental sample MimarksC
biotic_relationship 0..1 recommended
BIOTICRELATIONSHIPENUM		 Description of relationship(s) between the subject organism and other organis... MimarksC
seq_quality_check 0..1 recommended
SEQQUALITYCHECKENUM		 Indicate if the sequence has been called by automatic systems (none) or under... MimarksC
project_name 1..1
String		 Name of the project within which the sequencing was organized MimarksC, SymbiontAssociated
neg_cont_type 0..1 recommended
NEGCONTTYPEENUM		 The substance or equipment used as a negative control in an investigation MimarksC
chimera_check 0..1 recommended
String		 Tool(s) used for chimera checking, including version number and parameters, t... MimarksC
trophic_level 0..1 recommended
TROPHICLEVELENUM		 Trophic levels are the feeding position in a food chain MimarksC
pos_cont_type 0..1 recommended
String		 The substance, mixture, product, or apparatus used to verify that a process w... MimarksC
subspecf_gen_lin 0..1 recommended
String		 Information about the genetic distinctness of the sequenced organism below th... MimarksC
env_local_scale 1..1
String		 Report the entity or entities which are in the sample or specimen s local vic... MimarksC
samp_mat_process 0..1 recommended
String		 A brief description of any processing applied to the sample during or after r... MimarksC
depth 0..1 recommended
String		 The vertical distance below local surface MimarksC, SymbiontAssociated
samp_collect_method 0..1
String		 The method employed for collecting the sample MimarksC
env_medium 1..1
String		 Report the environmental material(s) immediately surrounding the sample or sp... MimarksC
samp_taxon_id 1..1
String		 NCBI taxon id of the sample MimarksC
geo_loc_name 1..1
String		 The geographical origin of the sample as defined by the country or sea name f... MimarksC, SymbiontAssociated
collection_date 1..1
Datetime		 The time of sampling, either as an instance (single point in time) or interva... MimarksC, SymbiontAssociated
seq_meth 1..1
String		 Sequencing machine used MimarksC
lat_lon 1..1
String		 The geographical origin of the sample as defined by latitude and longitude MimarksC, SymbiontAssociated
elev 0..1 recommended
String		 Elevation of the sampling site is its height above a fixed reference point, m... MimarksC, SymbiontAssociated
env_broad_scale 1..1
String		 Report the major environmental system the sample or specimen came from MimarksC
experimental_factor 0..*
String		 Variable aspects of an experiment design that can be used to describe an expe... MimarksC
target_gene 1..1
String		 Targeted gene or locus name for marker gene studies MimarksC
associated_resource 0..* recommended
String		 A related resource that is referenced, cited, or otherwise associated to the ... MimarksC
sop 0..* recommended
String		 Standard operating procedures used in assembly and/or annotation of genomes, ... MimarksC
host_subject_id 0..1
String		 A unique identifier by which each subject can be referred to, de-identified SymbiontAssociated
host_common_name 0..1
String		 Common name of the host SymbiontAssociated
host_taxid 0..1
String		 NCBI taxon id of the host, e SymbiontAssociated
host_dependence 1..1
HOSTDEPENDENCEENUM		 Type of host dependence for the symbiotic host organism to its host SymbiontAssociated
type_of_symbiosis 0..1 recommended
TYPEOFSYMBIOSISENUM		 Type of biological interaction established between the symbiotic host organis... SymbiontAssociated
sym_life_cycle_type 1..1
SYMLIFECYCLETYPEENUM		 Type of life cycle of the symbiotic host species (the thing being sampled) SymbiontAssociated
host_life_stage 1..1
String		 Description of life stage of host SymbiontAssociated
host_age 0..1
String		 Age of host at the time of sampling; relevant scale depends on species and st... SymbiontAssociated
urobiom_sex 0..1
UROBIOMSEXENUM		 Physical sex of the host SymbiontAssociated
mode_transmission 0..1 recommended
MODETRANSMISSIONENUM		 The process through which the symbiotic host organism entered the host from w... SymbiontAssociated
route_transmission 0..1
ROUTETRANSMISSIONENUM		 Description of path taken by the symbiotic host organism being sampled in ord... SymbiontAssociated
host_body_habitat 0..1
String		 Original body habitat where the sample was obtained from SymbiontAssociated
host_body_site 0..1
String		 Name of body site where the sample was obtained from, such as a specific orga... SymbiontAssociated
host_body_product 0..1
String		 Substance produced by the body, e SymbiontAssociated
host_tot_mass 0..1
String		 Total mass of the host at collection, the unit depends on host SymbiontAssociated
host_height 0..1
String		 The height of subject SymbiontAssociated
host_length 0..1
String		 The length of subject SymbiontAssociated
host_growth_cond 0..1
String		 Literature reference giving growth conditions of the host SymbiontAssociated
host_substrate 0..1
String		 The growth substrate of the host SymbiontAssociated
host_fam_rel 0..*
String		 Relationships to other hosts in the same study; can include multiple relation... SymbiontAssociated
host_infra_spec_name 0..1
String		 Taxonomic information about the host below subspecies level SymbiontAssociated
host_infra_spec_rank 0..1
String		 Taxonomic rank information about the host below subspecies level, such as var... SymbiontAssociated
host_genotype 0..1
String		 Observed genotype SymbiontAssociated
host_phenotype 0..1
String		 Phenotype of human or other host SymbiontAssociated
host_dry_mass 0..1
String		 Measurement of dry mass SymbiontAssociated
host_color 0..1
String		 The color of host SymbiontAssociated
host_shape 0..1
String		 Morphological shape of host SymbiontAssociated
gravidity 0..1
String		 Whether or not subject is gravid, and if yes date due or date post-conception... SymbiontAssociated
host_number 0..1
String		 Number of symbiotic host individuals pooled at the time of collection SymbiontAssociated
host_symbiont 0..*
String		 The taxonomic name of the organism(s) found living in mutualistic, commensali... SymbiontAssociated
host_specificity 0..1 recommended
HOSTSPECIFICITYENUM		 Level of specificity of symbiont-host interaction: e SymbiontAssociated
symbiont_host_role 0..1 recommended
SYMBIONTHOSTROLEENUM		 Role of the host in the life cycle of the symbiotic organism SymbiontAssociated
host_cellular_loc 0..1 recommended
HOSTCELLULARLOCENUM		 The localization of the symbiotic host organism within the host from which it... SymbiontAssociated
association_duration 0..1
String		 Time spent in host of the symbiotic organism at the time of sampling; relevan... SymbiontAssociated
host_of_host_coinf 0..1
String		 The taxonomic name of any coinfecting organism observed in a symbiotic relati... SymbiontAssociated
host_of_host_name 0..1
String		 Common name of the host of the symbiotic host organism SymbiontAssociated
host_of_host_env_loc 0..*
String		 For a symbiotic host organism the local anatomical environment within its hos... SymbiontAssociated
host_of_host_env_med 0..1
String		 Report the environmental material(s) immediately surrounding the symbiotic ho... SymbiontAssociated
host_of_host_taxid 0..1
String		 NCBI taxon id of the host of the symbiotic host organism SymbiontAssociated
host_of_host_sub_id 0..1
String		 A unique identifier by which each host of the symbiotic host organism subject... SymbiontAssociated
host_of_host_disease 0..*
String		 List of diseases with which the host of the symbiotic host organism has been ... SymbiontAssociated
host_of_host_fam_rel 0..*
String		 Familial relationship of the host of the symbiotic host organisms to other ho... SymbiontAssociated
host_of_host_infname 0..1
String		 Taxonomic name information of the host of the symbiotic host organism below s... SymbiontAssociated
host_of_host_infrank 0..1
String		 Taxonomic rank information about the host of the symbiotic host organism belo... SymbiontAssociated
host_of_host_geno 0..1
String		 Observed genotype of the host of the symbiotic host organism SymbiontAssociated
host_of_host_pheno 0..1
String		 Phenotype of the host of the symbiotic host organism SymbiontAssociated
host_of_host_gravid 0..1
String		 Whether or not the host of the symbiotic host organism is gravid, and if yes ... SymbiontAssociated
host_of_host_totmass 0..1
String		 Total mass of the host of the symbiotic host organism at collection, the unit... SymbiontAssociated
chem_administration 0..*
String		 List of chemical compounds administered to the host or site where sampling oc... SymbiontAssociated
perturbation 0..*
String		 Type of perturbation, e SymbiontAssociated
salinity 0..1
String		 The total concentration of all dissolved salts in a liquid or solid sample SymbiontAssociated
oxy_stat_samp 0..1
OXYSTATSAMPENUM		 Oxygenation status of sample SymbiontAssociated
organism_count 0..*
String		 Total cell count of any organism (or group of organisms) per gram, volume or ... SymbiontAssociated
samp_store_temp 0..1
String		 Temperature at which sample was stored, e SymbiontAssociated
samp_store_dur 0..1
String		 Duration for which the sample was stored SymbiontAssociated
samp_store_loc 0..1
String		 Location at which sample was stored, usually name of a specific freezer/room SymbiontAssociated
samp_store_sol 0..1
String		 Solution within which sample was stored, if any SymbiontAssociated
misc_param 0..*
String		 Any other measurement performed or parameter collected, that is not listed he... SymbiontAssociated

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/mixs-6-2-rc

LinkML Source

Direct

name: MimarksCSymbiontAssociated
description: MIxS data that complies with the MimarksC checklist and the SymbiontAssociated
  Extension
title: MimarksC combined with SymbiontAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: SymbiontAssociated
mixins:
- MimarksC
class_uri: MIXS:0010009_0016023

Induced

name: MimarksCSymbiontAssociated
description: MIxS data that complies with the MimarksC checklist and the SymbiontAssociated
  Extension
title: MimarksC combined with SymbiontAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: SymbiontAssociated
mixins:
- MimarksC
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-6-2-rc
    keywords:
    - sample
    slot_uri: MIXS:0001107
    multivalued: false
    alias: samp_name
    owner: MimarksCSymbiontAssociated
    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
  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: https://w3id.org/mixs-6-2-rc
    string_serialization: FWD:{dna};REV:{dna}
    slot_uri: MIXS:0000046
    multivalued: false
    alias: pcr_primers
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    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: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000038
    multivalued: false
    alias: nucl_acid_amp
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    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()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: 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: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000045
    multivalued: false
    alias: target_subfragment
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  temp:
    name: temp
    description: Temperature of the sample at the time of sampling
    title: temperature
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000113
    multivalued: false
    alias: temp
    owner: MimarksCSymbiontAssociated
    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
    required: false
    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
  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: https://w3id.org/mixs-6-2-rc
    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: MimarksCSymbiontAssociated
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  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: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000037
    multivalued: false
    alias: nucl_acid_ext
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    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()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  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: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000001
    multivalued: false
    alias: samp_size
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    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
  isol_growth_condt:
    name: isol_growth_condt
    description: Publication reference in the form of pubmed ID (pmid), digital object
      identifier (doi) or url for isolation and growth condition specifications of
      the organism/material
    title: isolation and growth condition
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000003
    multivalued: false
    alias: isol_growth_condt
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - MimarksC
    - Agriculture
    range: string
    required: true
    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()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  alt:
    name: alt
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000094
    multivalued: false
    alias: alt
    owner: MimarksCSymbiontAssociated
    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
  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: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000026
    multivalued: true
    alias: source_mat_id
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - SymbiontAssociated
    range: string
    required: false
    recommended: true
  extrachrom_elements:
    name: extrachrom_elements
    description: Do plasmids exist of significant phenotypic consequence (e.g. ones
      that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids
      (borrelia has 15+ plasmids)
    title: extrachromosomal elements
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000023
    multivalued: false
    alias: extrachrom_elements
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MimarksC
    range: integer
    required: false
    recommended: false
  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: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000111
    multivalued: false
    alias: samp_vol_we_dna_ext
    owner: MimarksCSymbiontAssociated
    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
    required: false
    recommended: false
    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
  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: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000015
    multivalued: false
    alias: rel_to_oxygen
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    range: REL_TO_OXYGEN_ENUM
    recommended: true
  samp_collect_device:
    name: samp_collect_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
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000002
    multivalued: false
    alias: samp_collect_device
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  biotic_relationship:
    name: biotic_relationship
    description: Description of relationship(s) between the subject organism and other
      organism(s) it is associated with. E.g., parasite on species X; mutualist with
      species Y. The target organism is the subject of the relationship, and the other
      organism(s) is the object
    title: observed biotic relationship
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000028
    multivalued: false
    alias: biotic_relationship
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - MimarksC
    - Miuvig
    - Agriculture
    range: BIOTIC_RELATIONSHIP_ENUM
    recommended: 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: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000051
    multivalued: false
    alias: seq_quality_check
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: SEQ_QUALITY_CHECK_ENUM
    recommended: 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-6-2-rc
    keywords:
    - project
    slot_uri: MIXS:0000092
    multivalued: false
    alias: project_name
    owner: MimarksCSymbiontAssociated
    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
  neg_cont_type:
    name: neg_cont_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration or text
    description: The substance or equipment used as a negative control in an investigation
    title: negative control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - type
    slot_uri: MIXS:0001321
    multivalued: false
    alias: neg_cont_type
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: NEG_CONT_TYPE_ENUM
    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: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000052
    multivalued: false
    alias: chimera_check
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  trophic_level:
    name: trophic_level
    description: Trophic levels are the feeding position in a food chain. Microbes
      can be a range of producers (e.g. chemolithotroph)
    title: trophic level
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000032
    multivalued: false
    alias: trophic_level
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MimarksC
    - Agriculture
    range: TROPHIC_LEVEL_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
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - type
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    multivalued: false
    alias: pos_cont_type
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    recommended: true
  subspecf_gen_lin:
    name: subspecf_gen_lin
    description: Information about the genetic distinctness of the sequenced organism
      below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any
      relevant genetic typing schemes like Group I plasmid. Subspecies should not
      be recorded in this term, but in the NCBI taxonomy. Supply both the lineage
      name and the lineage rank separated by a colon, e.g., biovar:abc123
    title: subspecific genetic lineage
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{rank name}:{text}'
    slot_uri: MIXS:0000020
    multivalued: false
    alias: subspecf_gen_lin
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - MimarksC
    - FoodFoodProductionFacility
    range: string
    recommended: true
  env_local_scale:
    name: env_local_scale
    annotations:
      Expected_value:
        tag: Expected_value
        value: Environmental entities having causal influences upon the entity at
          time of sampling
    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
    examples:
    - value: hillside [ENVO:01000333]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - context
    - environmental
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000013
    multivalued: false
    alias: env_local_scale
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: 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: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000016
    multivalued: false
    alias: samp_mat_process
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  depth:
    name: depth
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000018
    multivalued: false
    alias: depth
    owner: MimarksCSymbiontAssociated
    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
  samp_collect_method:
    name: samp_collect_method
    description: The method employed for collecting the sample
    title: sample collection method
    examples:
    - value: swabbing
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0001225
    multivalued: false
    alias: samp_collect_method
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    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
  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
    examples:
    - value: bluegrass field soil [ENVO:00005789]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - environmental
    slot_uri: MIXS:0000014
    multivalued: false
    alias: env_medium
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: 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
    examples:
    - value: Gut Metagenome [NCBITaxon:749906]
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - dna
    - identifier
    - sample
    - taxon
    slot_uri: MIXS:0001320
    multivalued: false
    alias: samp_taxon_id
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$
    structured_pattern:
      syntax: ^{text} \[{NCBItaxon_id}\]$
      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-6-2-rc
    keywords:
    - geographic
    - location
    slot_uri: MIXS:0000010
    multivalued: false
    alias: geo_loc_name
    owner: MimarksCSymbiontAssociated
    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-6-2-rc
    keywords:
    - date
    slot_uri: MIXS:0000011
    multivalued: false
    alias: collection_date
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: datetime
    required: 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
    examples:
    - value: 454 Genome Sequencer FLX [OBI:0000702]
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - method
    slot_uri: MIXS:0000050
    multivalued: false
    alias: seq_meth
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
    structured_pattern:
      syntax: ^{text}|({termLabel} \[{termID}\])$
      interpolated: true
      partial_match: true
  lat_lon:
    name: lat_lon
    annotations:
      Expected_value:
        tag: Expected_value
        value: decimal degrees,  limit to 8 decimal points
    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)
    examples:
    - value: 50.586825 6.408977
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - geographic
    - location
    string_serialization: '{float} {float}'
    slot_uri: MIXS:0000009
    alias: lat_lon
    owner: MimarksCSymbiontAssociated
    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
  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: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000093
    multivalued: false
    alias: elev
    owner: MimarksCSymbiontAssociated
    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
  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
    examples:
    - value: rangeland biome [ENVO:01000247]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - context
    - environmental
    slot_uri: MIXS:0000012
    multivalued: false
    alias: env_broad_scale
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  experimental_factor:
    name: experimental_factor
    description: Variable aspects of an experiment design that 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)
    title: experimental factor
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000008
    multivalued: true
    alias: experimental_factor
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  target_gene:
    name: target_gene
    description: Targeted gene or locus name for marker gene studies
    title: target gene
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000044
    multivalued: false
    alias: target_gene
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    required: true
  associated_resource:
    name: associated_resource
    annotations:
      Expected_value:
        tag: Expected_value
        value: reference to resource
    description: A related resource that is referenced, cited, or otherwise associated
      to the sequence
    title: relevant electronic resources
    examples:
    - value: http://www.earthmicrobiome.org/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - resource
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000091
    multivalued: true
    alias: associated_resource
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    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: https://w3id.org/mixs-6-2-rc
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000090
    multivalued: true
    alias: sop
    owner: MimarksCSymbiontAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: 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-6-2-rc
    slot_uri: MIXS:0000861
    multivalued: false
    alias: host_subject_id
    owner: MimarksCSymbiontAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  host_common_name:
    name: host_common_name
    description: Common name of the host
    title: host common name
    examples:
    - value: trematode
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000248
    multivalued: false
    alias: host_common_name
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  host_taxid:
    name: host_taxid
    description: NCBI taxon id of the host, e.g. 9606
    title: host taxid
    examples:
    - value: '395013'
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{integer}'
    slot_uri: MIXS:0000250
    multivalued: false
    alias: host_taxid
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - host
    - host.
    slot_uri: MIXS:0001315
    multivalued: false
    alias: host_dependence
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: HOST_DEPENDENCE_ENUM
    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-6-2-rc
    keywords:
    - symbiosis
    - type
    slot_uri: MIXS:0001307
    multivalued: false
    alias: type_of_symbiosis
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: TYPE_OF_SYMBIOSIS_ENUM
    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-6-2-rc
    keywords:
    - host
    - host.
    - life
    - organism
    - symbiosis
    - type
    slot_uri: MIXS:0001300
    multivalued: false
    alias: sym_life_cycle_type
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: SYM_LIFE_CYCLE_TYPE_ENUM
    required: true
  host_life_stage:
    name: host_life_stage
    description: Description of life stage of host
    title: host life stage
    examples:
    - value: redia
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000251
    multivalued: false
    alias: host_life_stage
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    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: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000255
    multivalued: false
    alias: host_age
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
    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-6-2-rc
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000862
    multivalued: false
    alias: urobiom_sex
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: UROBIOM_SEX_ENUM
    required: false
    recommended: 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
    examples:
    - value: horizontal:castrator
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0001312
    alias: mode_transmission
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: MODE_TRANSMISSION_ENUM
    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-6-2-rc
    keywords:
    - route
    slot_uri: MIXS:0001316
    multivalued: false
    alias: route_transmission
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: ROUTE_TRANSMISSION_ENUM
    required: false
    recommended: false
  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-6-2-rc
    slot_uri: MIXS:0000866
    multivalued: false
    alias: host_body_habitat
    owner: MimarksCSymbiontAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: 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...). 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-6-2-rc
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000867
    multivalued: false
    alias: host_body_site
    owner: MimarksCSymbiontAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - body
    - host
    - host.
    - product
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000888
    multivalued: false
    alias: host_body_product
    owner: MimarksCSymbiontAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000263
    multivalued: false
    alias: host_tot_mass
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_height:
    name: host_height
    description: The height of subject
    title: host height
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000264
    multivalued: false
    alias: host_height
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
    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
    description: The length of subject
    title: host length
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000256
    multivalued: false
    alias: host_length
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000871
    multivalued: false
    alias: host_growth_cond
    owner: MimarksCSymbiontAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000252
    multivalued: false
    alias: host_substrate
    owner: MimarksCSymbiontAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  host_fam_rel:
    name: host_fam_rel
    description: Relationships to other hosts in the same study; can include multiple
      relationships
    title: host family relationship
    examples:
    - value: clone;P15
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0000872
    multivalued: true
    alias: host_fam_rel
    owner: MimarksCSymbiontAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000253
    multivalued: false
    alias: host_infra_spec_name
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - host
    - host.
    - rank
    slot_uri: MIXS:0000254
    multivalued: false
    alias: host_infra_spec_rank
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  host_genotype:
    name: host_genotype
    description: Observed genotype
    title: host genotype
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000365
    multivalued: false
    alias: host_genotype
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  host_phenotype:
    name: host_phenotype
    description: Phenotype of human or other host. Use terms from the phenotypic quality
      ontology (pato) or the Human Phenotype Ontology (HP)
    title: host phenotype
    examples:
    - value: soldier
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000874
    multivalued: false
    alias: host_phenotype
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - dry
    - host
    - host.
    - mass
    slot_uri: MIXS:0000257
    multivalued: false
    alias: host_dry_mass
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
    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-6-2-rc
    slot_uri: MIXS:0000260
    multivalued: false
    alias: host_color
    owner: MimarksCSymbiontAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  host_shape:
    name: host_shape
    description: Morphological shape of host
    title: host shape
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000261
    multivalued: false
    alias: host_shape
    owner: MimarksCSymbiontAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc
    string_serialization: '{boolean};{timestamp}'
    slot_uri: MIXS:0000875
    multivalued: false
    alias: gravidity
    owner: MimarksCSymbiontAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - host
    - host.
    - number
    string_serialization: '{float} m'
    slot_uri: MIXS:0001305
    multivalued: false
    alias: host_number
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: 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. 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-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0001298
    multivalued: true
    alias: host_symbiont
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: 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
    examples:
    - value: species-specific
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - host
    - host.
    slot_uri: MIXS:0001308
    multivalued: false
    alias: host_specificity
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: HOST_SPECIFICITY_ENUM
    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-6-2-rc
    keywords:
    - host
    - host.
    - symbiosis
    slot_uri: MIXS:0001303
    multivalued: false
    alias: symbiont_host_role
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: SYMBIONT_HOST_ROLE_ENUM
    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-6-2-rc
    keywords:
    - host
    - host.
    - location
    slot_uri: MIXS:0001313
    alias: host_cellular_loc
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: HOST_CELLULAR_LOC_ENUM
    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-6-2-rc
    keywords:
    - duration
    - host
    - host.
    - period
    slot_uri: MIXS:0001299
    multivalued: false
    alias: association_duration
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
    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-6-2-rc
    keywords:
    - host
    - host.
    - observed
    - organism
    string_serialization: '{text}'
    slot_uri: MIXS:0001310
    multivalued: false
    alias: host_of_host_coinf
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: 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
    examples:
    - value: snail
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - host
    - host.
    - symbiosis
    slot_uri: MIXS:0001324
    alias: host_of_host_name
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - context
    - environmental
    - host
    - host.
    - symbiosis
    string_serialization: small intestine [UBERON:0002108]
    slot_uri: MIXS:0001325
    multivalued: true
    alias: host_of_host_env_loc
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - environmental
    - host
    - host.
    - symbiosis
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0001326
    alias: host_of_host_env_med
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - host
    - host.
    - identifier
    - symbiosis
    - taxon
    string_serialization: '{integer}'
    slot_uri: MIXS:0001306
    multivalued: false
    alias: host_of_host_taxid
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: 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
    examples:
    - value: H3
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - host
    - host.
    - identifier
    - symbiosis
    slot_uri: MIXS:0001327
    multivalued: false
    alias: host_of_host_sub_id
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - disease
    - host
    - host.
    - status
    - symbiosis
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0001319
    multivalued: true
    alias: host_of_host_disease
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - family
    - host
    - host.
    - relationship
    - symbiosis
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0001328
    multivalued: true
    alias: host_of_host_fam_rel
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc
    keywords:
    - host
    - host.
    - symbiosis
    slot_uri: MIXS:0001329
    multivalued: false
    alias: host_of_host_infname
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc
    keywords:
    - host
    - host.
    - rank
    - symbiosis
    slot_uri: MIXS:0001330
    multivalued: false
    alias: host_of_host_infrank
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc
    keywords:
    - host
    - host.
    - symbiosis
    slot_uri: MIXS:0001331
    multivalued: false
    alias: host_of_host_geno
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - host
    - host.
    - symbiosis
    string_serialization: '{term}'
    slot_uri: MIXS:0001332
    multivalued: false
    alias: host_of_host_pheno
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - host
    - host.
    - symbiosis
    string_serialization: '{boolean};{timestamp}'
    slot_uri: MIXS:0001333
    multivalued: false
    alias: host_of_host_gravid
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc
    keywords:
    - host
    - host.
    - mass
    - symbiosis
    - total
    slot_uri: MIXS:0001334
    multivalued: false
    alias: host_of_host_totmass
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
    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
    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: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}];{timestamp}'
    slot_uri: MIXS:0000751
    multivalued: true
    alias: chem_administration
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000754
    multivalued: true
    alias: perturbation
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - salinity
    slot_uri: MIXS:0000183
    multivalued: false
    alias: salinity
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000753
    multivalued: false
    alias: oxy_stat_samp
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - Air
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: OXY_STAT_SAMP_ENUM
    required: false
    recommended: 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
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
    slot_uri: MIXS:0000103
    multivalued: true
    alias: organism_count
    owner: MimarksCSymbiontAssociated
    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
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - sample
    - storage
    - temperature
    slot_uri: MIXS:0000110
    multivalued: false
    alias: samp_store_temp
    owner: MimarksCSymbiontAssociated
    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
    required: false
    recommended: false
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000116
    multivalued: false
    alias: samp_store_dur
    owner: MimarksCSymbiontAssociated
    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
    required: false
    recommended: false
    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
    description: Location at which sample was stored, usually name of a specific freezer/room
    title: sample storage location
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000755
    multivalued: false
    alias: samp_store_loc
    owner: MimarksCSymbiontAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - sample
    - storage
    string_serialization: '{text}'
    slot_uri: MIXS:0001317
    multivalued: false
    alias: samp_store_sol
    owner: MimarksCSymbiontAssociated
    domain_of:
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - parameter
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    multivalued: true
    alias: misc_param
    owner: MimarksCSymbiontAssociated
    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
    required: false
    recommended: false
class_uri: MIXS:0010009_0016023