Class: MisagHumanAssociated

MIxS data that complies with the Misag checklist and the HumanAssociated Extension

Inheritance

Extension
- HumanAssociated
  - MisagHumanAssociated [ Misag]

Slots

Name	Cardinality and Range	Description	Inheritance
assembly_software	1..1 String	Tool(s) used for assembly, including version number and parameters	Misag
temp	0..1 recommended String	Temperature of the sample at the time of sampling	Misag, HumanAssociated
assembly_qual	1..1 String	The assembly quality category is based on sets of criteria outlined for each ...	Misag
collection_date	1..1 Datetime	The time of sampling, either as an instance (single point in time) or interva...	Misag
nucl_acid_ext	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...	Misag
tax_ident	1..1 TAXIDENTENUM	The phylogenetic marker(s) used to assign an organism name to the SAG or MAG	Misag
samp_vol_we_dna_ext	0..1 String	Volume (ml) or mass (g) of total collected sample processed for DNA extractio...	Misag, HumanAssociated
compl_appr	0..1 COMPLAPPRENUM	The approach used to determine the completeness of a given genomic assembly, ...	Misag
contam_screen_input	0..1 CONTAMSCREENINPUTENUM	The type of sequence data used as input	Misag
sort_tech	1..1 SORTTECHENUM	Method used to sort/isolate cells or particles of interest	Misag
trna_ext_software	0..1 String	Tools used for tRNA identification	Misag
source_mat_id	0..* recommended String	A unique identifier assigned to a material sample (as defined by http://rs	Misag
tax_class	0..1 String	Method used for taxonomic classification, along with reference database used,...	Misag
ref_biomaterial	0..1 String	Primary publication if isolated before genome publication; otherwise, primary...	Misag
sim_search_meth	0..1 String	Tool used to compare ORFs with database, along with version and cutoffs used	Misag
number_contig	0..1 Integer	Total number of contigs in the cleaned/submitted assembly that makes up a giv...	Misag
env_broad_scale	1..1 String	Report the major environmental system the sample or specimen came from	Misag
wga_amp_appr	1..1 WGAAMPAPPRENUM	Method used to amplify genomic DNA in preparation for sequencing	Misag
project_name	1..1 String	Name of the project within which the sequencing was organized	Misag, HumanAssociated
x16s_recover_software	0..1 String	Tools used for 16S rRNA gene extraction	Misag
contam_screen_param	0..1 String	Specific parameters used in the decontamination sofware, such as reference da...	Misag
samp_collect_device	0..1 recommended String	The device used to collect an environmental sample	Misag
sc_lysis_approach	1..1 SCLYSISAPPROACHENUM	Method used to free DNA from interior of the cell(s) or particle(s)	Misag
lib_size	0..1 recommended Integer	Total number of clones in the library prepared for the project	Misag
compl_score	1..1 String	Completeness score is typically based on either the fraction of markers found...	Misag
samp_collect_method	0..1 recommended String	The method employed for collecting the sample	Misag
lib_layout	0..1 recommended LIBLAYOUTENUM	Specify whether to expect single, paired, or other configuration of reads	Misag
annot	0..1 String	Tool used for annotation, or for cases where annotation was provided by a com...	Misag
seq_meth	1..1 String	Sequencing machine used	Misag
depth	0..1 recommended String	The vertical distance below local surface	Misag
samp_size	0..1 recommended String	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...	Misag
pos_cont_type	0..1 recommended String	The substance, mixture, product, or apparatus used to verify that a process w...	Misag
size_frac	0..1 String	Filtering pore size used in sample preparation	Misag
alt	0..1 recommended String	Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba...	Misag
geo_loc_name	1..1 String	The geographical origin of the sample as defined by the country or sea name f...	Misag
trnas	0..1 String	The total number of tRNAs identified from the SAG or MAG	Misag
feat_pred	0..1 String	Method used to predict UViGs features such as ORFs, integration site, etc	Misag
neg_cont_type	0..1 recommended NEGCONTTYPEENUM	The substance or equipment used as a negative control in an investigation	Misag
env_local_scale	1..1 String	Report the entity or entities which are in the sample or specimen s local vic...	Misag
wga_amp_kit	0..1 String	Kit used to amplify genomic DNA in preparation for sequencing	Misag
samp_mat_process	0..1 recommended String	A brief description of any processing applied to the sample during or after r...	Misag
experimental_factor	0..* recommended String	Variable aspects of an experiment design that can be used to describe an expe...	Misag
samp_taxon_id	1..1 String	NCBI taxon id of the sample	Misag
nucl_acid_amp	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...	Misag
lib_screen	0..1 recommended String	Specific enrichment or screening methods applied before and/or after creating...	Misag
contam_score	1..1 Float	The contamination score is based on the fraction of single-copy genes that ar...	Misag
x16s_recover	0..1 Boolean	Can a 16S gene be recovered from the submitted SAG or MAG?	Misag
samp_name	1..1 String	A local identifier or name that for the material sample used for extracting n...	Misag, HumanAssociated
env_medium	1..1 String	Report the environmental material(s) immediately surrounding the sample or sp...	Misag
lib_vector	0..1 recommended String	Cloning vector type(s) used in construction of libraries	Misag
ref_db	0..1 String	List of database(s) used for ORF annotation, along with version number and re...	Misag
elev	0..1 recommended String	Elevation of the sampling site is its height above a fixed reference point, m...	Misag
lat_lon	1..1 String	The geographical origin of the sample as defined by latitude and longitude	Misag
compl_software	1..1 String	Tools used for completion estimate, i	Misag
lib_reads_seqd	0..1 recommended Integer	Total number of clones sequenced from the library	Misag
mid	0..1 recommended String	Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe...	Misag
decontam_software	0..1 String	Tool(s) used in contamination screening	Misag
sc_lysis_method	0..1 String	Name of the kit or standard protocol used for cell(s) or particle(s) lysis	Misag
rel_to_oxygen	0..1 RELTOOXYGENENUM	Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ...	Misag
assembly_name	0..1 recommended String	Name/version of the assembly provided by the submitter that is used in the ge...	Misag
adapters	0..1 recommended String	Adapters provide priming sequences for both amplification and sequencing of t...	Misag
associated_resource	0..* recommended String	A related resource that is referenced, cited, or otherwise associated to the ...	Misag
sop	0..* recommended String	Standard operating procedures used in assembly and/or annotation of genomes, ...	Misag
host_subject_id	0..1 String	A unique identifier by which each subject can be referred to, de-identified	HumanAssociated
host_age	0..1 String	Age of host at the time of sampling; relevant scale depends on species and st...	HumanAssociated
host_sex	0..1 String	Gender or physical sex of the host	HumanAssociated
host_disease_stat	0..1 String	List of diseases with which the host has been diagnosed; can include multiple...	HumanAssociated
ihmc_medication_code	0..* Integer	Can include multiple medication codes	HumanAssociated
chem_administration	0..* String	List of chemical compounds administered to the host or site where sampling oc...	HumanAssociated
host_body_site	0..1 String	Name of body site where the sample was obtained from, such as a specific orga...	HumanAssociated
host_body_product	0..1 String	Substance produced by the body, e	HumanAssociated
host_tot_mass	0..1 String	Total mass of the host at collection, the unit depends on host	HumanAssociated
host_height	0..1 String	The height of subject	HumanAssociated
host_diet	0..* String	Type of diet depending on the host, for animals omnivore, herbivore etc	HumanAssociated
host_last_meal	0..* String	Content of last meal and time since feeding; can include multiple values	HumanAssociated
host_fam_rel	0..* String	Relationships to other hosts in the same study; can include multiple relation...	HumanAssociated
host_genotype	0..1 String	Observed genotype	HumanAssociated
host_phenotype	0..1 String	Phenotype of human or other host	HumanAssociated
host_body_temp	0..1 String	Core body temperature of the host when sample was collected	HumanAssociated
smoker	0..1 Boolean	Specification of smoking status	HumanAssociated
host_hiv_stat	0..1 String	HIV status of subject, if yes HAART initiation status should also be indicate...	HumanAssociated
drug_usage	0..* String	Any drug used by subject and the frequency of usage; can include multiple dru...	HumanAssociated
host_body_mass_index	0..1 String	Body mass index, calculated as weight/(height)squared	HumanAssociated
diet_last_six_month	0..1 String	Specification of major diet changes in the last six months, if yes the change...	HumanAssociated
weight_loss_3_month	0..1 String	Specification of weight loss in the last three months, if yes should be furth...	HumanAssociated
ethnicity	0..* String	A category of people who identify with each other, usually on the basis of pr...	HumanAssociated
host_occupation	0..1 String	Most frequent job performed by subject	HumanAssociated
pet_farm_animal	0..* String	Specification of presence of pets or farm animals in the environment of subje...	HumanAssociated
travel_out_six_month	0..* String	Specification of the countries travelled in the last six months; can include ...	HumanAssociated
twin_sibling	0..1 Boolean	Specification of twin sibling presence	HumanAssociated
medic_hist_perform	0..1 Boolean	Whether full medical history was collected	HumanAssociated
study_complt_stat	0..1 String	Specification of study completion status, if no the reason should be specifie...	HumanAssociated
pulmonary_disord	0..* String	History of pulmonary disorders; can include multiple disorders	HumanAssociated
nose_throat_disord	0..* String	History of nose-throat disorders; can include multiple disorders, The terms ...	HumanAssociated
blood_blood_disord	0..* String	History of blood disorders; can include multiple disorders	HumanAssociated
host_pulse	0..1 String	Resting pulse, measured as beats per minute	HumanAssociated
gestation_state	0..1 String	Specification of the gestation state	HumanAssociated
maternal_health_stat	0..1 String	Specification of the maternal health status	HumanAssociated
foetal_health_stat	0..1 String	Specification of foetal health status, should also include abortion	HumanAssociated
amniotic_fluid_color	0..1 String	Specification of the color of the amniotic fluid sample	HumanAssociated
kidney_disord	0..* String	History of kidney disorders; can include multiple disorders	HumanAssociated
urogenit_tract_disor	0..* String	History of urogenital tract disorders; can include multiple disorders	HumanAssociated
urine_collect_meth	0..1 URINECOLLECTMETHENUM	Specification of urine collection method	HumanAssociated
perturbation	0..* String	Type of perturbation, e	HumanAssociated
salinity	0..1 String	The total concentration of all dissolved salts in a liquid or solid sample	HumanAssociated
oxy_stat_samp	0..1 OXYSTATSAMPENUM	Oxygenation status of sample	HumanAssociated
organism_count	0..* String	Total cell count of any organism (or group of organisms) per gram, volume or ...	HumanAssociated
samp_store_temp	0..1 String	Temperature at which sample was stored, e	HumanAssociated
samp_store_dur	0..1 String	Duration for which the sample was stored	HumanAssociated
host_symbiont	0..* String	The taxonomic name of the organism(s) found living in mutualistic, commensali...	HumanAssociated
samp_store_loc	0..1 String	Location at which sample was stored, usually name of a specific freezer/room	HumanAssociated
misc_param	0..* String	Any other measurement performed or parameter collected, that is not listed he...	HumanAssociated

Usages

used by	used in	type	used
MixsCompliantData	misag_human_associated_data	range	MisagHumanAssociated

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	MIXS:0010010_0016003
native	mixs_6_2_rc:MisagHumanAssociated

LinkML Source

Direct

name: MisagHumanAssociated
description: MIxS data that complies with the Misag checklist and the HumanAssociated
  Extension
title: Misag combined with HumanAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: HumanAssociated
mixins:
- Misag
class_uri: MIXS:0010010_0016003

Induced

name: MisagHumanAssociated
description: MIxS data that complies with the Misag checklist and the HumanAssociated
  Extension
title: Misag combined with HumanAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: HumanAssociated
mixins:
- Misag
attributes:
  assembly_software:
    name: assembly_software
    description: Tool(s) used for assembly, including version number and parameters
    title: assembly software
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000058
    multivalued: false
    alias: assembly_software
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    required: 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
  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: MisagHumanAssociated
    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
  assembly_qual:
    name: assembly_qual
    description: 'The assembly quality category is based on sets of criteria outlined
      for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
      contiguous sequence per replicon without gaps or ambiguities with a consensus
      error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
      where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes
      and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no
      review of assembly other than reporting of standard assembly statistics. Low
      Quality Draft:Many fragments with little to no review of assembly other than
      reporting of standard assembly statistics. Assembly statistics include, but
      are not limited to total assembly size, number of contigs, contig N50/L50, and
      maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence
      per replicon without gaps or ambiguities, with extensive manual review and editing
      to annotate putative gene functions and transcriptional units. High-quality
      draft genome: One or multiple fragments, totaling   90% of the expected genome
      or replicon sequence or predicted complete. Genome fragment(s): One or multiple
      fragments, totalling < 90% of the expected genome or replicon sequence, or for
      which no genome size could be estimated'
    title: assembly quality
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '[Finished genome|High-quality draft genome|Medium-quality
      draft genome|Low-quality draft genome|Genome fragment(s)]'
    slot_uri: MIXS:0000056
    multivalued: false
    alias: assembly_qual
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - 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
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000011
    multivalued: false
    alias: collection_date
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: datetime
    required: 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: MisagHumanAssociated
    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
  tax_ident:
    name: tax_ident
    description: The phylogenetic marker(s) used to assign an organism name to the
      SAG or MAG
    title: taxonomic identity marker
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000053
    alias: tax_ident
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: TAX_IDENT_ENUM
    required: 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: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000111
    multivalued: false
    alias: samp_vol_we_dna_ext
    owner: MisagHumanAssociated
    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
  compl_appr:
    name: compl_appr
    description: The approach used to determine the completeness of a given genomic
      assembly, which would typically make use of a set of conserved marker genes
      or a closely related reference genome. For UViG completeness, include reference
      genome or group used, and contig feature suggesting a complete genome
    title: completeness approach
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000071
    alias: compl_appr
    owner: MisagHumanAssociated
    domain_of:
    - Mimag
    - Misag
    - Miuvig
    range: COMPL_APPR_ENUM
    required: false
    recommended: false
  contam_screen_input:
    name: contam_screen_input
    description: The type of sequence data used as input
    title: contamination screening input
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000005
    multivalued: false
    alias: contam_screen_input
    owner: MisagHumanAssociated
    domain_of:
    - Mimag
    - Misag
    range: CONTAM_SCREEN_INPUT_ENUM
    required: false
    recommended: false
  sort_tech:
    name: sort_tech
    description: Method used to sort/isolate cells or particles of interest
    title: sorting technology
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000075
    multivalued: false
    alias: sort_tech
    owner: MisagHumanAssociated
    domain_of:
    - Misag
    - Miuvig
    range: SORT_TECH_ENUM
    required: true
  trna_ext_software:
    name: trna_ext_software
    description: Tools used for tRNA identification
    title: tRNA extraction software
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000068
    multivalued: false
    alias: trna_ext_software
    owner: MisagHumanAssociated
    domain_of:
    - Mimag
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
    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
  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: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - SymbiontAssociated
    range: string
    recommended: true
  tax_class:
    name: tax_class
    description: Method used for taxonomic classification, along with reference database
      used, classification rank, and thresholds used to classify new genomes
    title: taxonomic classification
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000064
    multivalued: false
    alias: tax_class
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  ref_biomaterial:
    name: ref_biomaterial
    description: Primary publication if isolated before genome publication; otherwise,
      primary genome report
    title: reference for biomaterial
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000025
    multivalued: false
    alias: ref_biomaterial
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    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()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  sim_search_meth:
    name: sim_search_meth
    description: Tool used to compare ORFs with database, along with version and cutoffs
      used
    title: similarity search method
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000063
    multivalued: false
    alias: sim_search_meth
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
    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
  number_contig:
    name: number_contig
    description: Total number of contigs in the cleaned/submitted assembly that makes
      up a given genome, SAG, MAG, or UViG
    title: number of contigs
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000060
    multivalued: false
    alias: number_contig
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: integer
    required: false
    recommended: false
  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
    slot_uri: MIXS:0000012
    multivalued: false
    alias: env_broad_scale
    owner: MisagHumanAssociated
    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
  wga_amp_appr:
    name: wga_amp_appr
    description: Method used to amplify genomic DNA in preparation for sequencing
    title: WGA amplification approach
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000055
    multivalued: false
    alias: wga_amp_appr
    owner: MisagHumanAssociated
    domain_of:
    - Misag
    - Miuvig
    range: WGA_AMP_APPR_ENUM
    required: true
  project_name:
    name: project_name
    description: Name of the project within which the sequencing was organized
    title: project name
    examples:
    - value: Forest soil metagenome
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000092
    multivalued: false
    alias: project_name
    owner: MisagHumanAssociated
    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
  x16s_recover_software:
    name: x16s_recover_software
    description: Tools used for 16S rRNA gene extraction
    title: 16S recovery software
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000066
    multivalued: false
    alias: x16s_recover_software
    owner: MisagHumanAssociated
    domain_of:
    - Mimag
    - Misag
    range: string
    required: false
    recommended: false
    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
  contam_screen_param:
    name: contam_screen_param
    description: Specific parameters used in the decontamination sofware, such as
      reference database, coverage, and kmers. Combinations of these parameters may
      also be used, i.e. kmer and coverage, or reference database and kmer
    title: contamination screening parameters
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '[ref db|kmer|coverage|combination];{text|integer}'
    slot_uri: MIXS:0000073
    multivalued: false
    alias: contam_screen_param
    owner: MisagHumanAssociated
    domain_of:
    - Mimag
    - Misag
    range: string
    required: false
    recommended: false
  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: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
  sc_lysis_approach:
    name: sc_lysis_approach
    description: Method used to free DNA from interior of the cell(s) or particle(s)
    title: single cell or viral particle lysis approach
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000076
    multivalued: false
    alias: sc_lysis_approach
    owner: MisagHumanAssociated
    domain_of:
    - Misag
    - Miuvig
    range: SC_LYSIS_APPROACH_ENUM
    required: true
  lib_size:
    name: lib_size
    description: Total number of clones in the library prepared for the project
    title: library size
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000039
    multivalued: false
    alias: lib_size
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    recommended: true
  compl_score:
    name: compl_score
    description: 'Completeness score is typically based on either the fraction of
      markers found as compared to a database or the percent of a genome found as
      compared to a closely related reference genome. High Quality Draft: >90%, Medium
      Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated
      completeness scores'
    title: completeness score
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '[high|med|low];{percentage}'
    slot_uri: MIXS:0000069
    multivalued: false
    alias: compl_score
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: string
    required: 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: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - 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()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: true
  lib_layout:
    name: lib_layout
    description: Specify whether to expect single, paired, or other configuration
      of reads
    title: library layout
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000041
    multivalued: false
    alias: lib_layout
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: LIB_LAYOUT_ENUM
    recommended: true
  annot:
    name: annot
    description: Tool used for annotation, or for cases where annotation was provided
      by a community jamboree or model organism database rather than by a specific
      submitter
    title: annotation
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000059
    multivalued: false
    alias: annot
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    required: false
    recommended: false
  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
    slot_uri: MIXS:0000050
    multivalued: false
    alias: seq_meth
    owner: MisagHumanAssociated
    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
  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: MisagHumanAssociated
    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_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: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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
  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
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    multivalued: false
    alias: pos_cont_type
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    recommended: true
  size_frac:
    name: size_frac
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    multivalued: false
    alias: size_frac
    owner: MisagHumanAssociated
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  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: MisagHumanAssociated
    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
  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
    slot_uri: MIXS:0000010
    multivalued: false
    alias: geo_loc_name
    owner: MisagHumanAssociated
    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
  trnas:
    name: trnas
    description: The total number of tRNAs identified from the SAG or MAG
    title: number of standard tRNAs extracted
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{integer}'
    slot_uri: MIXS:0000067
    multivalued: false
    alias: trnas
    owner: MisagHumanAssociated
    domain_of:
    - Mimag
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  feat_pred:
    name: feat_pred
    description: Method used to predict UViGs features such as ORFs, integration site,
      etc
    title: feature prediction
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000061
    multivalued: false
    alias: feat_pred
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
    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
  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
    slot_uri: MIXS:0001321
    multivalued: false
    alias: neg_cont_type
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: NEG_CONT_TYPE_ENUM
    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
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000013
    multivalued: false
    alias: env_local_scale
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
  wga_amp_kit:
    name: wga_amp_kit
    description: Kit used to amplify genomic DNA in preparation for sequencing
    title: WGA amplification kit
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000006
    multivalued: false
    alias: wga_amp_kit
    owner: MisagHumanAssociated
    domain_of:
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  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: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: 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: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  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
    slot_uri: MIXS:0001320
    multivalued: false
    alias: samp_taxon_id
    owner: MisagHumanAssociated
    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
  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: MisagHumanAssociated
    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
  lib_screen:
    name: lib_screen
    description: Specific enrichment or screening methods applied before and/or after
      creating libraries
    title: library screening strategy
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000043
    multivalued: false
    alias: lib_screen
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  contam_score:
    name: contam_score
    description: 'The contamination score is based on the fraction of single-copy
      genes that are observed more than once in a query genome. The following scores
      are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low
      Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be
      deposited into any of the public databases'
    title: contamination score
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000072
    multivalued: false
    alias: contam_score
    owner: MisagHumanAssociated
    domain_of:
    - Mimag
    - Misag
    range: float
    required: true
  x16s_recover:
    name: x16s_recover
    description: Can a 16S gene be recovered from the submitted SAG or MAG?
    title: 16S recovered
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000065
    multivalued: false
    alias: x16s_recover
    owner: MisagHumanAssociated
    domain_of:
    - Mimag
    - Misag
    range: boolean
    required: false
    recommended: false
  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
    slot_uri: MIXS:0001107
    multivalued: false
    alias: samp_name
    owner: MisagHumanAssociated
    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
  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
    slot_uri: MIXS:0000014
    multivalued: false
    alias: env_medium
    owner: MisagHumanAssociated
    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
  lib_vector:
    name: lib_vector
    description: Cloning vector type(s) used in construction of libraries
    title: library vector
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000042
    multivalued: false
    alias: lib_vector
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  ref_db:
    name: ref_db
    description: List of database(s) used for ORF annotation, along with version number
      and reference to website or publication
    title: reference database(s)
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{database};{version};{reference}'
    slot_uri: MIXS:0000062
    multivalued: false
    alias: ref_db
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  elev:
    name: elev
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit
    title: elevation
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000093
    multivalued: false
    alias: elev
    owner: MisagHumanAssociated
    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
  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
    string_serialization: '{float} {float}'
    slot_uri: MIXS:0000009
    alias: lat_lon
    owner: MisagHumanAssociated
    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
  compl_software:
    name: compl_software
    description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
    title: completeness software
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{software};{version}'
    slot_uri: MIXS:0000070
    multivalued: false
    alias: compl_software
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: string
    required: true
  lib_reads_seqd:
    name: lib_reads_seqd
    description: Total number of clones sequenced from the library
    title: library reads sequenced
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000040
    multivalued: false
    alias: lib_reads_seqd
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    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: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000047
    multivalued: false
    alias: mid
    owner: MisagHumanAssociated
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^[ACGTRKSYMWBHDVN]+$
    structured_pattern:
      syntax: ^{ambiguous_nucleotides}$
      interpolated: true
      partial_match: true
  decontam_software:
    name: decontam_software
    description: Tool(s) used in contamination screening
    title: decontamination software
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '[checkm/refinem|anvi''o|prodege|bbtools:decontaminate.sh|acdc|combination]'
    slot_uri: MIXS:0000074
    multivalued: false
    alias: decontam_software
    owner: MisagHumanAssociated
    domain_of:
    - Mimag
    - Misag
    range: string
    required: false
    recommended: false
  sc_lysis_method:
    name: sc_lysis_method
    description: Name of the kit or standard protocol used for cell(s) or particle(s)
      lysis
    title: single cell or viral particle lysis kit protocol
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000054
    multivalued: false
    alias: sc_lysis_method
    owner: MisagHumanAssociated
    domain_of:
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  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: MisagHumanAssociated
    domain_of:
    - MigsBa
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    range: REL_TO_OXYGEN_ENUM
    required: false
    recommended: false
  assembly_name:
    name: assembly_name
    description: Name/version of the assembly provided by the submitter that is used
      in the genome browsers and in the community
    title: assembly name
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text} {text}'
    slot_uri: MIXS:0000057
    multivalued: false
    alias: assembly_name
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    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: https://w3id.org/mixs-6-2-rc
    string_serialization: '{dna};{dna}'
    slot_uri: MIXS:0000048
    multivalued: false
    alias: adapters
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: 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
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000091
    multivalued: true
    alias: associated_resource
    owner: MisagHumanAssociated
    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: MisagHumanAssociated
    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: MPI123
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000861
    multivalued: false
    alias: host_subject_id
    owner: MisagHumanAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
    required: false
    recommended: 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
    examples:
    - value: 30 years
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000255
    multivalued: false
    alias: host_age
    owner: MisagHumanAssociated
    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_sex:
    name: host_sex
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration
    description: Gender or physical sex of the host
    title: host sex
    comments:
    - example of non-binary from Excel sheets does not match any of the enumerated
      values
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '[female|hermaphrodite|non-binary|male|transgender|transgender
      (female to male)|transgender (male to female)

      |undeclared]'
    slot_uri: MIXS:0000811
    alias: host_sex
    owner: MisagHumanAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
    required: false
    recommended: false
  host_disease_stat:
    name: host_disease_stat
    description: List of diseases with which the host has been diagnosed; can include
      multiple diagnoses. The value of the field depends on host; for humans the terms
      should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
      non-human host diseases are free text
    title: host disease status
    examples:
    - value: measles [DOID:8622]
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000031
    multivalued: false
    alias: host_disease_stat
    owner: MisagHumanAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    range: string
    required: false
    recommended: false
  ihmc_medication_code:
    name: ihmc_medication_code
    description: Can include multiple medication codes
    title: IHMC medication code
    examples:
    - value: '810'
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000884
    multivalued: true
    alias: ihmc_medication_code
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: integer
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}];{timestamp}'
    slot_uri: MIXS:0000751
    multivalued: true
    alias: chem_administration
    owner: MisagHumanAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    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: Lung parenchyma [fma27360]
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000867
    multivalued: false
    alias: host_body_site
    owner: MisagHumanAssociated
    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
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000888
    multivalued: false
    alias: host_body_product
    owner: MisagHumanAssociated
    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
    examples:
    - value: 65 kilogram
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000263
    multivalued: false
    alias: host_tot_mass
    owner: MisagHumanAssociated
    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
    examples:
    - value: 1.75 meter
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000264
    multivalued: false
    alias: host_height
    owner: MisagHumanAssociated
    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_diet:
    name: host_diet
    description: Type of diet depending on the host, for animals omnivore, herbivore
      etc., for humans high-fat, meditteranean etc.; can include multiple diet types
    title: host diet
    examples:
    - value: high-fat
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000869
    multivalued: true
    alias: host_diet
    owner: MisagHumanAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
    required: false
    recommended: 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
    examples:
    - value: french fries;P5H30M
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text};{duration}'
    slot_uri: MIXS:0000870
    multivalued: true
    alias: host_last_meal
    owner: MisagHumanAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    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: mother;ID298
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0000872
    multivalued: true
    alias: host_fam_rel
    owner: MisagHumanAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  host_genotype:
    name: host_genotype
    description: Observed genotype
    title: host genotype
    examples:
    - value: ST1
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000365
    multivalued: false
    alias: host_genotype
    owner: MisagHumanAssociated
    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: Tinnitus [HP:0000360]
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000874
    multivalued: false
    alias: host_phenotype
    owner: MisagHumanAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  host_body_temp:
    name: host_body_temp
    description: Core body temperature of the host when sample was collected
    title: host body temperature
    examples:
    - value: 36.5 degree Celsius
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000274
    multivalued: false
    alias: host_body_temp
    owner: MisagHumanAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    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
  smoker:
    name: smoker
    description: Specification of smoking status
    title: smoker
    examples:
    - value: 'yes'
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000262
    multivalued: false
    alias: smoker
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: boolean
    required: false
    recommended: false
  host_hiv_stat:
    name: host_hiv_stat
    annotations:
      Expected_value:
        tag: Expected_value
        value: HIV status;HAART initiation status
    description: HIV status of subject, if yes HAART initiation status should also
      be indicated as [YES or NO]
    title: host HIV status
    examples:
    - value: yes;yes
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{boolean};{boolean}'
    slot_uri: MIXS:0000265
    multivalued: false
    alias: host_hiv_stat
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  drug_usage:
    name: drug_usage
    annotations:
      Expected_value:
        tag: Expected_value
        value: drug name;frequency
    description: Any drug used by subject and the frequency of usage; can include
      multiple drugs used
    title: drug usage
    examples:
    - value: Lipitor;2/day
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text};{integer}/[year|month|week|day|hour]'
    slot_uri: MIXS:0000894
    multivalued: true
    alias: drug_usage
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  host_body_mass_index:
    name: host_body_mass_index
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: kilogram per square meter
    description: Body mass index, calculated as weight/(height)squared
    title: host body-mass index
    examples:
    - value: 22 kilogram per square meter
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000317
    multivalued: false
    alias: host_body_mass_index
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    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
  diet_last_six_month:
    name: diet_last_six_month
    annotations:
      Expected_value:
        tag: Expected_value
        value: diet change;current diet
    description: Specification of major diet changes in the last six months, if yes
      the change should be specified
    title: major diet change in last six months
    examples:
    - value: yes;vegetarian diet
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{boolean};{text}'
    slot_uri: MIXS:0000266
    multivalued: false
    alias: diet_last_six_month
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  weight_loss_3_month:
    name: weight_loss_3_month
    annotations:
      Expected_value:
        tag: Expected_value
        value: weight loss specification;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: kilogram, gram
    description: Specification of weight loss in the last three months, if yes should
      be further specified to include amount of weight loss
    title: weight loss in last three months
    examples:
    - value: yes;5 kilogram
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{boolean};{float} {unit}'
    slot_uri: MIXS:0000295
    multivalued: false
    alias: weight_loss_3_month
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  ethnicity:
    name: ethnicity
    annotations:
      Expected_value:
        tag: Expected_value
        value: text recommend from Wikipedia list
    description: A category of people who identify with each other, usually on the
      basis of presumed similarities such as a common language, ancestry, history,
      society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups
    title: ethnicity
    examples:
    - value: native american
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000895
    multivalued: true
    alias: ethnicity
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
    required: false
    recommended: false
  host_occupation:
    name: host_occupation
    description: Most frequent job performed by subject
    title: host occupation
    comments:
    - Couldn't convert host_occupation with value veterinary to integer
    - almost all host_occupation values in the NCBI biosample_set are strings, not
      integers
    examples:
    - value: veterinary
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000896
    alias: host_occupation
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
    required: false
    recommended: false
  pet_farm_animal:
    name: pet_farm_animal
    annotations:
      Expected_value:
        tag: Expected_value
        value: presence status;type of animal or pet
    description: Specification of presence of pets or farm animals in the environment
      of subject, if yes the animals should be specified; can include multiple animals
      present
    title: presence of pets or farm animals
    examples:
    - value: yes; 5 cats
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{boolean};{text}'
    slot_uri: MIXS:0000267
    multivalued: true
    alias: pet_farm_animal
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  travel_out_six_month:
    name: travel_out_six_month
    annotations:
      Expected_value:
        tag: Expected_value
        value: country name
    description: Specification of the countries travelled in the last six months;
      can include multiple travels
    title: travel outside the country in last six months
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000268
    multivalued: true
    alias: travel_out_six_month
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  twin_sibling:
    name: twin_sibling
    description: Specification of twin sibling presence
    title: twin sibling presence
    examples:
    - value: 'yes'
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000326
    multivalued: false
    alias: twin_sibling
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: boolean
    required: false
    recommended: false
  medic_hist_perform:
    name: medic_hist_perform
    description: Whether full medical history was collected
    title: medical history performed
    examples:
    - value: '1'
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000897
    multivalued: false
    alias: medic_hist_perform
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: boolean
    required: false
    recommended: false
  study_complt_stat:
    name: study_complt_stat
    annotations:
      Expected_value:
        tag: Expected_value
        value: YES or NO due to (1)adverse event (2) non-compliance (3) lost to follow
          up (4)other-specify
    description: Specification of study completion status, if no the reason should
      be specified
    title: study completion status
    examples:
    - value: no;non-compliance
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{boolean};[adverse event|non-compliance|lost to follow
      up|other-specify]'
    slot_uri: MIXS:0000898
    multivalued: false
    alias: study_complt_stat
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  pulmonary_disord:
    name: pulmonary_disord
    description: History of pulmonary disorders; can include multiple disorders. The
      terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
      lung disease (https://disease-ontology.org/?id=DOID:850)
    title: lung/pulmonary disorder
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000269
    multivalued: true
    alias: pulmonary_disord
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  nose_throat_disord:
    name: nose_throat_disord
    description: History of nose-throat disorders; can include multiple disorders,  The
      terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
      lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory
      tract disease (https://disease-ontology.org/?id=DOID:974)
    title: nose throat disorder
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000270
    multivalued: true
    alias: nose_throat_disord
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  blood_blood_disord:
    name: blood_blood_disord
    description: History of blood disorders; can include multiple disorders.  The
      terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
      hematopoietic system disease (https://disease-ontology.org/?id=DOID:74)
    title: blood/blood disorder
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000271
    multivalued: true
    alias: blood_blood_disord
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  host_pulse:
    name: host_pulse
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: beats per minute
    description: Resting pulse, measured as beats per minute
    title: host pulse
    examples:
    - value: 65 beats per minute
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000333
    multivalued: false
    alias: host_pulse
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    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
  gestation_state:
    name: gestation_state
    description: Specification of the gestation state
    title: amniotic fluid/gestation state
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000272
    multivalued: false
    alias: gestation_state
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  maternal_health_stat:
    name: maternal_health_stat
    description: Specification of the maternal health status
    title: amniotic fluid/maternal health status
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000273
    multivalued: false
    alias: maternal_health_stat
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  foetal_health_stat:
    name: foetal_health_stat
    description: Specification of foetal health status, should also include abortion
    title: amniotic fluid/foetal health status
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000275
    multivalued: false
    alias: foetal_health_stat
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  amniotic_fluid_color:
    name: amniotic_fluid_color
    description: Specification of the color of the amniotic fluid sample
    title: amniotic fluid/color
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000276
    multivalued: false
    alias: amniotic_fluid_color
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  kidney_disord:
    name: kidney_disord
    description: History of kidney disorders; can include multiple disorders. The
      terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
      kidney disease (https://disease-ontology.org/?id=DOID:557)
    title: urine/kidney disorder
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000277
    multivalued: true
    alias: kidney_disord
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  urogenit_tract_disor:
    name: urogenit_tract_disor
    description: History of urogenital tract disorders; can include multiple disorders.
      The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
      urinary system disease (https://disease-ontology.org/?id=DOID:18)
    title: urine/urogenital tract disorder
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000278
    multivalued: true
    alias: urogenit_tract_disor
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: string
    required: false
    recommended: false
  urine_collect_meth:
    name: urine_collect_meth
    description: Specification of urine collection method
    title: urine/collection method
    examples:
    - value: catheter
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000899
    multivalued: false
    alias: urine_collect_meth
    owner: MisagHumanAssociated
    domain_of:
    - HumanAssociated
    range: URINE_COLLECT_METH_ENUM
    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: MisagHumanAssociated
    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
    slot_uri: MIXS:0000183
    multivalued: false
    alias: salinity
    owner: MisagHumanAssociated
    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: MisagHumanAssociated
    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: MisagHumanAssociated
    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
    slot_uri: MIXS:0000110
    multivalued: false
    alias: samp_store_temp
    owner: MisagHumanAssociated
    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: MisagHumanAssociated
    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
  host_symbiont:
    name: host_symbiont
    description: The taxonomic name of the organism(s) found living in mutualistic,
      commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont
      can have its own symbionts. For example, parasites may have hyperparasites (=parasites
      of the parasite)
    title: observed host symbionts
    examples:
    - value: flukeworms
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0001298
    multivalued: true
    alias: host_symbiont
    owner: MisagHumanAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000755
    multivalued: false
    alias: samp_store_loc
    owner: MisagHumanAssociated
    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
  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
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    multivalued: true
    alias: misc_param
    owner: MisagHumanAssociated
    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:0010010_0016003