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Class: Human-skinMIMARKSSpecimen

Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-skin

URI: MIXS:Human-skinMIMARKSSpecimen

Inheritance

Slots

Name Cardinality and Range Description Inheritance
samp_name 1..1
String		 A local identifier or name that for the material sample used for extracting n... MIMARKSSpecimen
samp_taxon_id 1..1
String		 NCBI taxon id of the sample MIMARKSSpecimen
project_name 1..1
String		 Name of the project within which the sequencing was organized MIMARKSSpecimen
experimental_factor 0..1 recommended
String		 Experimental factors are essentially the variable aspects of an experiment de... MIMARKSSpecimen
lat_lon 1..1
String		 The geographical origin of the sample as defined by latitude and longitude Human-skin, MIMARKSSpecimen
geo_loc_name 1..1
String		 The geographical origin of the sample as defined by the country or sea name f... Human-skin, MIMARKSSpecimen
collection_date 1..1
Date		 The time of sampling, either as an instance (single point in time) or interva... Human-skin, MIMARKSSpecimen
neg_cont_type 0..1 recommended
NegContTypeEnum		 The substance or equipment used as a negative control in an investigation MIMARKSSpecimen
pos_cont_type 0..1 recommended
String		 The substance, mixture, product, or apparatus used to verify that a process w... MIMARKSSpecimen
env_broad_scale 1..1
String		 Report the major environmental system the sample or specimen came from Human-skin, MIMARKSSpecimen
env_local_scale 1..1
String		 Report the entity or entities which are in the sample or specimen’s local vic... Human-skin, MIMARKSSpecimen
env_medium 1..1
String		 Report the environmental material(s) immediately surrounding the sample or sp... Human-skin, MIMARKSSpecimen
source_mat_id 0..1 recommended
String		 A unique identifier assigned to a material sample (as defined by http://rs MIMARKSSpecimen
rel_to_oxygen 0..1
RelToOxygenEnum		 Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ... MIMARKSSpecimen
samp_collec_device 0..1 recommended
String		 The device used to collect an environmental sample MIMARKSSpecimen
samp_collec_method 0..1 recommended
String		 The method employed for collecting the sample MIMARKSSpecimen
samp_mat_process 0..1 recommended
String		 A brief description of any processing applied to the sample during or after r... MIMARKSSpecimen
size_frac 0..1
String		 Filtering pore size used in sample preparation MIMARKSSpecimen
samp_size 0..1 recommended
QuantityValue		 The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... MIMARKSSpecimen
samp_vol_we_dna_ext 0..1
QuantityValue		 Volume (ml) or mass (g) of total collected sample processed for DNA extractio... MIMARKSSpecimen
nucl_acid_ext 0..1 recommended
String		 A link to a literature reference, electronic resource or a standard operating... MIMARKSSpecimen
nucl_acid_amp 0..1 recommended
String		 A link to a literature reference, electronic resource or a standard operating... MIMARKSSpecimen
lib_size 0..1 recommended
Integer		 Total number of clones in the library prepared for the project MIMARKSSpecimen
lib_reads_seqd 0..1 recommended
Integer		 Total number of clones sequenced from the library MIMARKSSpecimen
lib_layout 0..1 recommended
LibLayoutEnum		 Specify whether to expect single, paired, or other configuration of reads MIMARKSSpecimen
lib_vector 0..1 recommended
String		 Cloning vector type(s) used in construction of libraries MIMARKSSpecimen
lib_screen 0..1 recommended
String		 Specific enrichment or screening methods applied before and/or after creating... MIMARKSSpecimen
target_gene 1..1
String		 Targeted gene or locus name for marker gene studies MIMARKSSpecimen
target_subfragment 0..1 recommended
String		 Name of subfragment of a gene or locus MIMARKSSpecimen
pcr_primers 0..1 recommended
String		 PCR primers that were used to amplify the sequence of the targeted gene, locu... MIMARKSSpecimen
mid 0..1 recommended
String		 Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe... MIMARKSSpecimen
adapters 0..1 recommended
String		 Adapters provide priming sequences for both amplification and sequencing of t... MIMARKSSpecimen
pcr_cond 0..1 recommended
String		 Description of reaction conditions and components of PCR in the form of 'init... MIMARKSSpecimen
seq_meth 1..1
String		 Sequencing machine used MIMARKSSpecimen
seq_quality_check 0..1 recommended
String		 Indicate if the sequence has been called by automatic systems (none) or under... MIMARKSSpecimen
chimera_check 0..1 recommended
String		 Tool(s) used for chimera checking, including version number and parameters, t... MIMARKSSpecimen
assembly_software 0..1 recommended
String		 Tool(s) used for assembly, including version number and parameters MIMARKSSpecimen
associated_resource 0..1 recommended
String		 A related resource that is referenced, cited, or otherwise associated to the ... MIMARKSSpecimen
sop 0..1 recommended
String		 Standard operating procedures used in assembly and/or annotation of genomes, ... MIMARKSSpecimen
depth 0..1
QuantityValue		 The vertical distance below local surface, e Human-skin
alt 0..1
QuantityValue		 Altitude is a term used to identify heights of objects such as airplanes, spa... Human-skin
elev 0..1
QuantityValue		 Elevation of the sampling site is its height above a fixed reference point, m... Human-skin
temp 0..1
QuantityValue		 Temperature of the sample at the time of sampling Human-skin
dermatology_disord 0..*
String		 History of dermatology disorders; can include multiple disorders Human-skin
time_since_last_wash 0..1
String		 Specification of the time since last wash Human-skin
dominant_hand 0..1
DominantHandEnum		 Dominant hand of the subject Human-skin
host_subject_id 0..1
String		 A unique identifier by which each subject can be referred to, de-identified Human-skin
host_age 0..1
QuantityValue		 Age of host at the time of sampling; relevant scale depends on species and st... Human-skin
host_sex 0..1
HostSexEnum		 Gender or physical sex of the host Human-skin
ihmc_medication_code 0..*
Integer		 Can include multiple medication codes Human-skin
chem_administration 0..*
String		 List of chemical compounds administered to the host or site where sampling oc... Human-skin
host_body_site 0..1
String		 Name of body site where the sample was obtained from, such as a specific orga... Human-skin
host_body_product 0..1
String		 Substance produced by the body, e Human-skin
host_tot_mass 0..1
QuantityValue		 Total mass of the host at collection, the unit depends on host Human-skin
host_height 0..1
QuantityValue		 The height of subject Human-skin
host_diet 0..*
String		 Type of diet depending on the host, for animals omnivore, herbivore etc Human-skin
host_last_meal 0..*
String		 Content of last meal and time since feeding; can include multiple values Human-skin
host_family_relation 0..*
String		 Familial relationships to other hosts in the same study; can include multiple... Human-skin
host_genotype 0..1
String		 Observed genotype Human-skin
host_phenotype 0..1
String		 Phenotype of human or other host Human-skin
host_body_temp 0..1
QuantityValue		 Core body temperature of the host when sample was collected Human-skin
host_body_mass_index 0..1
QuantityValue		 Body mass index, calculated as weight/(height)squared Human-skin
ethnicity 0..*
String		 A category of people who identify with each other, usually on the basis of pr... Human-skin
host_occupation 0..1
Integer		 Most frequent job performed by subject Human-skin
medic_hist_perform 0..1
String		 Whether full medical history was collected Human-skin
host_pulse 0..1
QuantityValue		 Resting pulse, measured as beats per minute Human-skin
perturbation 0..*
String		 Type of perturbation, e Human-skin
salinity 0..1
QuantityValue		 The total concentration of all dissolved salts in a liquid or solid sample Human-skin
oxy_stat_samp 0..1
OxyStatSampEnum		 Oxygenation status of sample Human-skin
organism_count 0..*
OrganismCountEnum		 Total cell count of any organism (or group of organisms) per gram, volume or ... Human-skin
samp_store_temp 0..1
QuantityValue		 Temperature at which sample was stored, e Human-skin
samp_store_dur 0..1
String		 Duration for which the sample was stored Human-skin
samp_store_loc 0..1
String		 Location at which sample was stored, usually name of a specific freezer/room Human-skin
host_symbiont 0..*
String		 The taxonomic name of the organism(s) found living in mutualistic, commensali... Human-skin
misc_param 0..*
String		 Any other measurement performed or parameter collected, that is not listed he... Human-skin

Identifier and Mapping Information

Schema Source

  • from schema: http://w3id.org/mixs

Mappings

Mapping Type Mapped Value
self MIXS:Human-skinMIMARKSSpecimen
native MIXS:Human-skinMIMARKSSpecimen

LinkML Source

Direct

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

Induced

name: human-skin MIMARKS specimen
description: 'Combinatorial checklist Minimal Information about a Marker Specimen:
  specimen with environmental package human-skin'
from_schema: http://w3id.org/mixs
is_a: human-skin
mixins:
- MIMARKS specimen
attributes:
  samp_name:
    name: samp_name
    description: A local identifier or name that for the material sample used for
      extracting nucleic acids, and subsequent sequencing. It can refer either to
      the original material collected or to any derived sub-samples. It can have any
      format, but we suggest that you make it concise, unique and consistent within
      your lab, and as informative as possible. INSDC requires every sample name from
      a single Submitter to be unique. Use of a globally unique identifier for the
      field source_mat_id is recommended in addition to sample_name.
    title: sample name
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{text}'
    slot_uri: MIXS:0001107
    multivalued: false
    alias: samp_name
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
  samp_taxon_id:
    name: samp_taxon_id
    description: NCBI taxon id of the sample.  Maybe be a single taxon or mixed taxa
      sample. Use 'synthetic metagenome’ for mock community/positive controls, or
      'blank sample' for negative controls.
    title: Taxonomy ID of DNA sample
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{text} [NCBI:txid]'
    slot_uri: MIXS:0001320
    multivalued: false
    alias: samp_taxon_id
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
  project_name:
    name: project_name
    description: Name of the project within which the sequencing was organized
    title: project name
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{text}'
    slot_uri: MIXS:0000092
    multivalued: false
    alias: project_name
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
  experimental_factor:
    name: experimental_factor
    description: Experimental factors are essentially the variable aspects of an experiment
      design which can be used to describe an experiment, or set of experiments, in
      an increasingly detailed manner. This field accepts ontology terms from Experimental
      Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For
      a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;
      for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
    title: experimental factor
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000008
    multivalued: false
    alias: experimental_factor
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  lat_lon:
    name: lat_lon
    description: The geographical origin of the sample as defined by latitude and
      longitude. The values should be reported in decimal degrees and in WGS84 system
    title: geographic location (latitude and longitude)
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{float} {float}'
    slot_uri: MIXS:0000009
    multivalued: false
    alias: lat_lon
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  geo_loc_name:
    name: geo_loc_name
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name. Country or sea names should be chosen
      from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
      (http://purl.bioontology.org/ontology/GAZ)
    title: geographic location (country and/or sea,region)
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{term}: {term}, {text}'
    slot_uri: MIXS:0000010
    multivalued: false
    alias: geo_loc_name
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  collection_date:
    name: collection_date
    description: 'The time of sampling, either as an instance (single point in time)
      or interval. In case no exact time is available, the date/time can be right
      truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
      2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
    title: collection date
    from_schema: http://w3id.org/mixs
    is_a: environment field
    slot_uri: MIXS:0000011
    multivalued: false
    alias: collection_date
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: date
    required: true
  neg_cont_type:
    name: neg_cont_type
    description: The substance or equipment used as a negative control in an investigation
    title: negative control type
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    slot_uri: MIXS:0001321
    multivalued: false
    alias: neg_cont_type
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: neg_cont_type_enum
    recommended: true
  pos_cont_type:
    name: pos_cont_type
    description: The substance, mixture, product, or apparatus used to verify that
      a process which is part of an investigation delivers a true positive.
    title: positive control type
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    multivalued: false
    alias: pos_cont_type
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  env_broad_scale:
    name: env_broad_scale
    description: 'Report the major environmental system the sample or specimen came
      from. The system(s) identified should have a coarse spatial grain, to provide
      the general environmental context of where the sampling was done (e.g. in the
      desert or a rainforest). We recommend using subclasses of EnvO’s biome class:  http://purl.obolibrary.org/obo/ENVO_00000428.
      EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: broad-scale environmental context
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    multivalued: false
    alias: env_broad_scale
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  env_local_scale:
    name: env_local_scale
    description: 'Report the entity or entities which are in the sample or specimen’s
      local vicinity and which you believe have significant causal influences on your
      sample or specimen. We recommend using EnvO terms which are of smaller spatial
      grain than your entry for env_broad_scale. Terms, such as anatomical sites,
      from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON)
      are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'
    title: local environmental context
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000013
    multivalued: false
    alias: env_local_scale
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  env_medium:
    name: env_medium
    description: 'Report the environmental material(s) immediately surrounding the
      sample or specimen at the time of sampling. We recommend using subclasses of
      ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
      documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
      . Terms from other OBO ontologies are permissible as long as they reference
      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
      (e.g. a tree, a leaf, a table top).'
    title: environmental medium
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000014
    multivalued: false
    alias: env_medium
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  source_mat_id:
    name: source_mat_id
    description: A unique identifier assigned to a material sample (as defined by
      http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
      digital record of a material sample) used for extracting nucleic acids, and
      subsequent sequencing. The identifier can refer either to the original material
      collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
      /bio_material, or /culture_collection may or may not share the same value as
      the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
      may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
      sampled tissue with the same identifier. However, the /culture_collection qualifier
      may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
      would refer to an identifier from some derived culture from which the nucleic
      acids were extracted (e.g. xatc123 or ark:/2154/R2).
    title: source material identifiers
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{text}'
    slot_uri: MIXS:0000026
    multivalued: false
    alias: source_mat_id
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  rel_to_oxygen:
    name: rel_to_oxygen
    description: Is this organism an aerobe, anaerobe? Please note that aerobic and
      anaerobic are valid descriptors for microbial environments
    title: relationship to oxygen
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000015
    multivalued: false
    alias: rel_to_oxygen
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS bacteria
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    range: rel_to_oxygen_enum
    required: false
  samp_collec_device:
    name: samp_collec_device
    description: The device used to collect an environmental sample. This field accepts
      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
    title: sample collection device
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000002
    multivalued: false
    alias: samp_collec_device
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  samp_collec_method:
    name: samp_collec_method
    description: The method employed for collecting the sample.
    title: sample collection method
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001225
    multivalued: false
    alias: samp_collec_method
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  samp_mat_process:
    name: samp_mat_process
    description: A brief description of any processing applied to the sample during
      or after retrieving the sample from environment, or a link to the relevant protocol(s)
      performed.
    title: sample material processing
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{text}'
    slot_uri: MIXS:0000016
    multivalued: false
    alias: samp_mat_process
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  size_frac:
    name: size_frac
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    multivalued: false
    alias: size_frac
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  samp_size:
    name: samp_size
    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
      sample collected.
    title: amount or size of sample collected
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000001
    multivalued: false
    alias: samp_size
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: quantity value
    recommended: true
  samp_vol_we_dna_ext:
    name: samp_vol_we_dna_ext
    description: 'Volume (ml) or mass (g) of total collected sample processed for
      DNA extraction. Note: total sample collected should be entered under the term
      Sample Size (MIXS:0000001).'
    title: sample volume or weight for DNA extraction
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000111
    multivalued: false
    alias: samp_vol_we_dna_ext
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: quantity value
    required: false
  nucl_acid_ext:
    name: nucl_acid_ext
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the material separation to recover
      the nucleic acid fraction from a sample
    title: nucleic acid extraction
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000037
    multivalued: false
    alias: nucl_acid_ext
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  nucl_acid_amp:
    name: nucl_acid_amp
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the enzymatic amplification (PCR,
      TMA, NASBA) of specific nucleic acids
    title: nucleic acid amplification
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000038
    multivalued: false
    alias: nucl_acid_amp
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  lib_size:
    name: lib_size
    description: Total number of clones in the library prepared for the project
    title: library size
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000039
    multivalued: false
    alias: lib_size
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: integer
    recommended: true
  lib_reads_seqd:
    name: lib_reads_seqd
    description: Total number of clones sequenced from the library
    title: library reads sequenced
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000040
    multivalued: false
    alias: lib_reads_seqd
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: integer
    recommended: true
  lib_layout:
    name: lib_layout
    description: Specify whether to expect single, paired, or other configuration
      of reads
    title: library layout
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000041
    multivalued: false
    alias: lib_layout
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: lib_layout_enum
    recommended: true
  lib_vector:
    name: lib_vector
    description: Cloning vector type(s) used in construction of libraries
    title: library vector
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000042
    multivalued: false
    alias: lib_vector
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  lib_screen:
    name: lib_screen
    description: Specific enrichment or screening methods applied before and/or after
      creating libraries
    title: library screening strategy
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000043
    multivalued: false
    alias: lib_screen
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  target_gene:
    name: target_gene
    description: Targeted gene or locus name for marker gene studies
    title: target gene
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000044
    multivalued: false
    alias: target_gene
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    required: true
  target_subfragment:
    name: target_subfragment
    description: Name of subfragment of a gene or locus. Important to e.g. identify
      special regions on marker genes like V6 on 16S rRNA
    title: target subfragment
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000045
    multivalued: false
    alias: target_subfragment
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    recommended: true
  pcr_primers:
    name: pcr_primers
    description: PCR primers that were used to amplify the sequence of the targeted
      gene, locus or subfragment. This field should contain all the primers used for
      a single PCR reaction if multiple forward or reverse primers are present in
      a single PCR reaction. The primer sequence should be reported in uppercase letters
    title: pcr primers
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: FWD:{dna};REV:{dna}
    slot_uri: MIXS:0000046
    multivalued: false
    alias: pcr_primers
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    recommended: true
  mid:
    name: mid
    description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
      used to specifically tag unique samples in a sequencing run. Sequence should
      be reported in uppercase letters
    title: multiplex identifiers
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{dna}'
    slot_uri: MIXS:0000047
    multivalued: false
    alias: mid
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  adapters:
    name: adapters
    description: Adapters provide priming sequences for both amplification and sequencing
      of the sample-library fragments. Both adapters should be reported; in uppercase
      letters
    title: adapters
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{dna};{dna}'
    slot_uri: MIXS:0000048
    multivalued: false
    alias: adapters
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  pcr_cond:
    name: pcr_cond
    description: Description of reaction conditions and components of PCR in the form
      of 'initial denaturation:94degC_1.5min; annealing=...'
    title: pcr conditions
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
      elongation:degrees_minutes;total cycles
    slot_uri: MIXS:0000049
    multivalued: false
    alias: pcr_cond
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    recommended: true
  seq_meth:
    name: seq_meth
    description: Sequencing machine used. Where possible the term should be taken
      from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).
    title: sequencing method
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000050
    multivalued: false
    alias: seq_meth
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
  seq_quality_check:
    name: seq_quality_check
    description: Indicate if the sequence has been called by automatic systems (none)
      or undergone a manual editing procedure (e.g. by inspecting the raw data or
      chromatograms). Applied only for sequences that are not submitted to SRA,ENA
      or DRA
    title: sequence quality check
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '[none|manually edited]'
    slot_uri: MIXS:0000051
    multivalued: false
    alias: seq_quality_check
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    recommended: true
  chimera_check:
    name: chimera_check
    description: Tool(s) used for chimera checking, including version number and parameters,
      to discover and remove chimeric sequences. A chimeric sequence is comprised
      of two or more phylogenetically distinct parent sequences.
    title: chimera check software
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{software};{version};{parameters}'
    slot_uri: MIXS:0000052
    multivalued: false
    alias: chimera_check
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    recommended: true
  assembly_software:
    name: assembly_software
    description: Tool(s) used for assembly, including version number and parameters
    title: assembly software
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{software};{version};{parameters}'
    slot_uri: MIXS:0000058
    multivalued: false
    alias: assembly_software
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  associated resource:
    name: associated resource
    description: A related resource that is referenced, cited, or otherwise associated
      to the sequence.
    title: relevant electronic resources
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID} | {DOI} | {URL}'
    slot_uri: MIXS:0000091
    multivalued: false
    alias: associated_resource
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  sop:
    name: sop
    description: Standard operating procedures used in assembly and/or annotation
      of genomes, metagenomes or environmental sequences
    title: relevant standard operating procedures
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000090
    multivalued: false
    alias: sop
    owner: human-skin MIMARKS specimen
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  depth:
    name: depth
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: The vertical distance below local surface, e.g. for sediment or soil
      samples depth is measured from sediment or soil surface, respectively. Depth
      can be reported as an interval for subsurface samples.
    title: depth
    examples:
    - value: 10 meter
    from_schema: http://w3id.org/mixs
    aliases:
    - depth
    is_a: environment field
    slot_uri: MIXS:0000018
    multivalued: false
    alias: depth
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
  alt:
    name: alt
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: Altitude is a term used to identify heights of objects such as airplanes,
      space shuttles, rockets, atmospheric balloons and heights of places such as
      atmospheric layers and clouds. It is used to measure the height of an object
      which is above the earth's surface. In this context, the altitude measurement
      is the vertical distance between the earth's surface above sea level and the
      sampled position in the air
    title: altitude
    examples:
    - value: 100 meter
    from_schema: http://w3id.org/mixs
    aliases:
    - altitude
    is_a: environment field
    slot_uri: MIXS:0000094
    multivalued: false
    alias: alt
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
  elev:
    name: elev
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit.
    title: elevation
    examples:
    - value: 100 meter
    from_schema: http://w3id.org/mixs
    aliases:
    - elevation
    is_a: environment field
    slot_uri: MIXS:0000093
    multivalued: false
    alias: elev
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
  temp:
    name: temp
    description: Temperature of the sample at the time of sampling.
    title: temperature
    from_schema: http://w3id.org/mixs
    is_a: environment field
    slot_uri: MIXS:0000113
    multivalued: false
    alias: temp
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
    required: false
  dermatology_disord:
    name: dermatology_disord
    description: History of dermatology disorders; can include multiple disorders.
      The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
      skin disease (https://disease-ontology.org/?id=DOID:37).
    title: dermatology disorder
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000284
    multivalued: true
    alias: dermatology_disord
    owner: human-skin MIMARKS specimen
    domain_of:
    - human-skin
    range: string
    required: false
  time_since_last_wash:
    name: time_since_last_wash
    description: Specification of the time since last wash
    title: time since last wash
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{duration}'
    slot_uri: MIXS:0000943
    multivalued: false
    alias: time_since_last_wash
    owner: human-skin MIMARKS specimen
    domain_of:
    - human-skin
    range: string
    required: false
  dominant_hand:
    name: dominant_hand
    description: Dominant hand of the subject
    title: dominant hand
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000944
    multivalued: false
    alias: dominant_hand
    owner: human-skin MIMARKS specimen
    domain_of:
    - human-skin
    range: dominant_hand_enum
    required: false
  host_subject_id:
    name: host_subject_id
    description: A unique identifier by which each subject can be referred to, de-identified.
    title: host subject id
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000861
    multivalued: false
    alias: host_subject_id
    owner: human-skin MIMARKS specimen
    domain_of:
    - symbiont-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    range: string
    required: false
  host_age:
    name: host_age
    description: Age of host at the time of sampling; relevant scale depends on species
      and study, e.g. Could be seconds for amoebae or centuries for trees
    title: host age
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000255
    multivalued: false
    alias: host_age
    owner: human-skin MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  host_sex:
    name: host_sex
    description: Gender or physical sex of the host.
    title: host sex
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000811
    multivalued: false
    alias: host_sex
    owner: human-skin MIMARKS specimen
    domain_of:
    - symbiont-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    range: host_sex_enum
    required: false
  ihmc_medication_code:
    name: ihmc_medication_code
    description: Can include multiple medication codes
    title: IHMC medication code
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000884
    multivalued: true
    alias: ihmc_medication_code
    owner: human-skin MIMARKS specimen
    domain_of:
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    range: integer
    required: false
  chem_administration:
    name: chem_administration
    description: List of chemical compounds administered to the host or site where
      sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
      include multiple compounds. For chemical entities of biological interest ontology
      (chebi) (v 163), http://purl.bioontology.org/ontology/chebi
    title: chemical administration
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]};{timestamp}'
    slot_uri: MIXS:0000751
    multivalued: true
    alias: chem_administration
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - air
    - agriculture
    range: string
    required: false
  host_body_site:
    name: host_body_site
    description: Name of body site where the sample was obtained from, such as a specific
      organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology
      (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,
      please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON
    title: host body site
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000867
    multivalued: false
    alias: host_body_site
    owner: human-skin MIMARKS specimen
    domain_of:
    - symbiont-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    range: string
    required: false
  host_body_product:
    name: host_body_product
    description: Substance produced by the body, e.g. Stool, mucus, where the sample
      was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy
      ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma
      or https://www.ebi.ac.uk/ols/ontologies/uberon
    title: host body product
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000888
    multivalued: false
    alias: host_body_product
    owner: human-skin MIMARKS specimen
    domain_of:
    - symbiont-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    range: string
    required: false
  host_tot_mass:
    name: host_tot_mass
    description: Total mass of the host at collection, the unit depends on host
    title: host total mass
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000263
    multivalued: false
    alias: host_tot_mass
    owner: human-skin MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  host_height:
    name: host_height
    description: The height of subject
    title: host height
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000264
    multivalued: false
    alias: host_height
    owner: human-skin MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  host_diet:
    name: host_diet
    description: Type of diet depending on the host, for animals omnivore, herbivore
      etc., for humans high-fat, meditteranean etc.; can include multiple diet types
    title: host diet
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000869
    multivalued: true
    alias: host_diet
    owner: human-skin MIMARKS specimen
    domain_of:
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    range: string
    required: false
  host_last_meal:
    name: host_last_meal
    description: Content of last meal and time since feeding; can include multiple
      values
    title: host last meal
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{duration}'
    slot_uri: MIXS:0000870
    multivalued: true
    alias: host_last_meal
    owner: human-skin MIMARKS specimen
    domain_of:
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    range: string
    required: false
  host_family_relation:
    name: host_family_relation
    description: Familial relationships to other hosts in the same study; can include
      multiple relationships
    title: host family relationship
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0000872
    multivalued: true
    alias: host_family_relation
    owner: human-skin MIMARKS specimen
    domain_of:
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    range: string
    required: false
  host_genotype:
    name: host_genotype
    description: Observed genotype
    title: host genotype
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000365
    multivalued: false
    alias: host_genotype
    owner: human-skin MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: string
    required: false
  host_phenotype:
    name: host_phenotype
    description: Phenotype of human or other host. For phenotypic quality ontology
      (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato.
      For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP
    title: host phenotype
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000874
    multivalued: false
    alias: host_phenotype
    owner: human-skin MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: string
    required: false
  host_body_temp:
    name: host_body_temp
    description: Core body temperature of the host when sample was collected
    title: host body temperature
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000274
    multivalued: false
    alias: host_body_temp
    owner: human-skin MIMARKS specimen
    domain_of:
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    range: quantity value
    required: false
  host_body_mass_index:
    name: host_body_mass_index
    description: Body mass index, calculated as weight/(height)squared
    title: host body-mass index
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000317
    multivalued: false
    alias: host_body_mass_index
    owner: human-skin MIMARKS specimen
    domain_of:
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    range: quantity value
    required: false
  ethnicity:
    name: ethnicity
    description: A category of people who identify with each other, usually on the
      basis of presumed similarities such as a common language, ancestry, history,
      society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups
    title: ethnicity
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000895
    multivalued: true
    alias: ethnicity
    owner: human-skin MIMARKS specimen
    domain_of:
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    range: string
    required: false
  host_occupation:
    name: host_occupation
    description: Most frequent job performed by subject
    title: host occupation
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000896
    multivalued: false
    alias: host_occupation
    owner: human-skin MIMARKS specimen
    domain_of:
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    range: integer
    required: false
  medic_hist_perform:
    name: medic_hist_perform
    description: Whether full medical history was collected
    title: medical history performed
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{boolean}'
    slot_uri: MIXS:0000897
    multivalued: false
    alias: medic_hist_perform
    owner: human-skin MIMARKS specimen
    domain_of:
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    range: string
    required: false
  host_pulse:
    name: host_pulse
    description: Resting pulse, measured as beats per minute
    title: host pulse
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000333
    multivalued: false
    alias: host_pulse
    owner: human-skin MIMARKS specimen
    domain_of:
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    range: quantity value
    required: false
  perturbation:
    name: perturbation
    description: Type of perturbation, e.g. chemical administration, physical disturbance,
      etc., coupled with perturbation regimen including how many times the perturbation
      was repeated, how long each perturbation lasted, and the start and end time
      of the entire perturbation period; can include multiple perturbation types
    title: perturbation
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000754
    multivalued: true
    alias: perturbation
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-farm environment
    - food-animal and animal feed
    - air
    - agriculture
    range: string
    required: false
  salinity:
    name: salinity
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000183
    multivalued: false
    alias: salinity
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - air
    range: quantity value
    required: false
  oxy_stat_samp:
    name: oxy_stat_samp
    description: Oxygenation status of sample
    title: oxygenation status of sample
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000753
    multivalued: false
    alias: oxy_stat_samp
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - air
    - agriculture
    range: oxy_stat_samp_enum
    required: false
  organism_count:
    name: organism_count
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000103
    multivalued: true
    alias: organism_count
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - built environment
    - air
    - agriculture
    range: organism_count_enum
    required: false
  samp_store_temp:
    name: samp_store_temp
    description: Temperature at which sample was stored, e.g. -80 degree Celsius
    title: sample storage temperature
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000110
    multivalued: false
    alias: samp_store_temp
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - air
    range: quantity value
    required: false
  samp_store_dur:
    name: samp_store_dur
    description: Duration for which the sample was stored
    title: sample storage duration
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{duration}'
    slot_uri: MIXS:0000116
    multivalued: false
    alias: samp_store_dur
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - air
    - agriculture
    range: string
    required: false
  samp_store_loc:
    name: samp_store_loc
    description: Location at which sample was stored, usually name of a specific freezer/room
    title: sample storage location
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000755
    multivalued: false
    alias: samp_store_loc
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - air
    - agriculture
    range: string
    required: false
  host_symbiont:
    name: host_symbiont
    description: The taxonomic name of the organism(s) found living in mutualistic,
      commensalistic, or parasitic symbiosis with the specific host.
    title: observed host symbionts
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001298
    multivalued: true
    alias: host_symbiont
    owner: human-skin MIMARKS specimen
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - agriculture
    range: string
    required: false
  misc_param:
    name: misc_param
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    multivalued: true
    alias: misc_param
    owner: human-skin MIMARKS specimen
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - air
    - agriculture
    range: string
    required: false