Class: MimagHumanVaginal

MIxS data that complies with the Mimag checklist and the HumanVaginal Extension

Inheritance

Extension
- HumanVaginal
  - MimagHumanVaginal [ Mimag]

Slots

Name	Cardinality and Range	Description	Inheritance
assembly_software	1..1 String	Tool(s) used for assembly, including version number and parameters	Mimag
temp	0..1 recommended String	Temperature of the sample at the time of sampling	HumanVaginal, Mimag
assembly_qual	1..1 String	The assembly quality category is based on sets of criteria outlined for each ...	Mimag
bin_param	1..1 BINPARAMENUM	The parameters that have been applied during the extraction of genomes from m...	Mimag
collection_date	1..1 Datetime	The time of sampling, either as an instance (single point in time) or interva...	Mimag
nucl_acid_ext	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...	Mimag
tax_ident	1..1 TAXIDENTENUM	The phylogenetic marker(s) used to assign an organism name to the SAG or MAG	Mimag
samp_vol_we_dna_ext	0..1 String	Volume (ml) or mass (g) of total collected sample processed for DNA extractio...	HumanVaginal, Mimag
contam_screen_input	0..1 CONTAMSCREENINPUTENUM	The type of sequence data used as input	Mimag
compl_appr	0..1 COMPLAPPRENUM	The approach used to determine the completeness of a given genomic assembly, ...	Mimag
trna_ext_software	0..1 String	Tools used for tRNA identification	Mimag
source_mat_id	0..* recommended String	A unique identifier assigned to a material sample (as defined by http://rs	Mimag
tax_class	0..1 String	Method used for taxonomic classification, along with reference database used,...	Mimag
bin_software	1..1 String	Tool(s) used for the extraction of genomes from metagenomic datasets, where p...	Mimag
ref_biomaterial	0..1 String	Primary publication if isolated before genome publication; otherwise, primary...	Mimag
sim_search_meth	0..1 String	Tool used to compare ORFs with database, along with version and cutoffs used	Mimag
number_contig	0..1 Integer	Total number of contigs in the cleaned/submitted assembly that makes up a giv...	Mimag
env_broad_scale	1..1 String	Report the major environmental system the sample or specimen came from	Mimag
project_name	1..1 String	Name of the project within which the sequencing was organized	HumanVaginal, Mimag
x16s_recover_software	0..1 String	Tools used for 16S rRNA gene extraction	Mimag
contam_screen_param	0..1 String	Specific parameters used in the decontamination sofware, such as reference da...	Mimag
samp_collect_device	0..1 recommended String	The device used to collect an environmental sample	Mimag
lib_size	0..1 recommended Integer	Total number of clones in the library prepared for the project	Mimag
compl_score	1..1 String	Completeness score is typically based on either the fraction of markers found...	Mimag
samp_collect_method	0..1 recommended String	The method employed for collecting the sample	Mimag
lib_layout	0..1 recommended LIBLAYOUTENUM	Specify whether to expect single, paired, or other configuration of reads	Mimag
annot	0..1 String	Tool used for annotation, or for cases where annotation was provided by a com...	Mimag
seq_meth	1..1 String	Sequencing machine used	Mimag
depth	0..1 recommended String	The vertical distance below local surface	Mimag
samp_size	0..1 recommended String	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...	Mimag
pos_cont_type	0..1 recommended String	The substance, mixture, product, or apparatus used to verify that a process w...	Mimag
size_frac	0..1 String	Filtering pore size used in sample preparation	Mimag
alt	0..1 recommended String	Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba...	Mimag
geo_loc_name	1..1 String	The geographical origin of the sample as defined by the country or sea name f...	Mimag
trnas	0..1 String	The total number of tRNAs identified from the SAG or MAG	Mimag
feat_pred	0..1 String	Method used to predict UViGs features such as ORFs, integration site, etc	Mimag
neg_cont_type	0..1 recommended NEGCONTTYPEENUM	The substance or equipment used as a negative control in an investigation	Mimag
env_local_scale	1..1 String	Report the entity or entities which are in the sample or specimen s local vic...	Mimag
samp_mat_process	0..1 recommended String	A brief description of any processing applied to the sample during or after r...	Mimag
experimental_factor	0..* recommended String	Variable aspects of an experiment design that can be used to describe an expe...	Mimag
samp_taxon_id	1..1 String	NCBI taxon id of the sample	Mimag
nucl_acid_amp	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...	Mimag
lib_screen	0..1 recommended String	Specific enrichment or screening methods applied before and/or after creating...	Mimag
contam_score	1..1 Float	The contamination score is based on the fraction of single-copy genes that ar...	Mimag
x16s_recover	0..1 Boolean	Can a 16S gene be recovered from the submitted SAG or MAG?	Mimag
samp_name	1..1 String	A local identifier or name that for the material sample used for extracting n...	HumanVaginal, Mimag
env_medium	1..1 String	Report the environmental material(s) immediately surrounding the sample or sp...	Mimag
lib_vector	0..1 recommended String	Cloning vector type(s) used in construction of libraries	Mimag
mag_cov_software	0..1 MAGCOVSOFTWAREENUM	Tool(s) used to determine the genome coverage if coverage is used as a binnin...	Mimag
ref_db	0..1 String	List of database(s) used for ORF annotation, along with version number and re...	Mimag
elev	0..1 recommended String	Elevation of the sampling site is its height above a fixed reference point, m...	Mimag
lat_lon	1..1 String	The geographical origin of the sample as defined by latitude and longitude	Mimag
compl_software	1..1 String	Tools used for completion estimate, i	Mimag
lib_reads_seqd	0..1 recommended Integer	Total number of clones sequenced from the library	Mimag
mid	0..1 recommended String	Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe...	Mimag
decontam_software	0..1 String	Tool(s) used in contamination screening	Mimag
reassembly_bin	0..1 Boolean	Has an assembly been performed on a genome bin extracted from a metagenomic a...	Mimag
rel_to_oxygen	0..1 RELTOOXYGENENUM	Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ...	Mimag
assembly_name	0..1 recommended String	Name/version of the assembly provided by the submitter that is used in the ge...	Mimag
adapters	0..1 recommended String	Adapters provide priming sequences for both amplification and sequencing of t...	Mimag
associated_resource	0..* recommended String	A related resource that is referenced, cited, or otherwise associated to the ...	Mimag
sop	0..* recommended String	Standard operating procedures used in assembly and/or annotation of genomes, ...	Mimag
menarche	0..1 Datetime	Date of most recent menstruation	HumanVaginal
sexual_act	0..1 String	Current sexual partner and frequency of sex	HumanVaginal
pregnancy	0..1 Datetime	Date due of pregnancy	HumanVaginal
douche	0..1 Datetime	Date of most recent douche	HumanVaginal
birth_control	0..1 String	Specification of birth control medication used	HumanVaginal
menopause	0..1 Datetime	Date of onset of menopause	HumanVaginal
hrt	0..1 Datetime	Whether subject had hormone replacement theraphy, and if yes start date	HumanVaginal
hysterectomy	0..1 Boolean	Specification of whether hysterectomy was performed	HumanVaginal
gynecologic_disord	0..* String	History of gynecological disorders; can include multiple disorders	HumanVaginal
urogenit_disord	0..* String	History of urogenital disorders, can include multiple disorders	HumanVaginal
host_subject_id	0..1 String	A unique identifier by which each subject can be referred to, de-identified	HumanVaginal
host_age	0..1 String	Age of host at the time of sampling; relevant scale depends on species and st...	HumanVaginal
host_sex	0..1 String	Gender or physical sex of the host	HumanVaginal
host_disease_stat	0..1 String	List of diseases with which the host has been diagnosed; can include multiple...	HumanVaginal
ihmc_medication_code	0..* Integer	Can include multiple medication codes	HumanVaginal
chem_administration	0..* String	List of chemical compounds administered to the host or site where sampling oc...	HumanVaginal
host_body_site	0..1 String	Name of body site where the sample was obtained from, such as a specific orga...	HumanVaginal
host_body_product	0..1 String	Substance produced by the body, e	HumanVaginal
host_tot_mass	0..1 String	Total mass of the host at collection, the unit depends on host	HumanVaginal
host_height	0..1 String	The height of subject	HumanVaginal
host_diet	0..* String	Type of diet depending on the host, for animals omnivore, herbivore etc	HumanVaginal
host_last_meal	0..* String	Content of last meal and time since feeding; can include multiple values	HumanVaginal
host_fam_rel	0..* String	Relationships to other hosts in the same study; can include multiple relation...	HumanVaginal
host_genotype	0..1 String	Observed genotype	HumanVaginal
host_phenotype	0..1 String	Phenotype of human or other host	HumanVaginal
host_body_temp	0..1 String	Core body temperature of the host when sample was collected	HumanVaginal
host_body_mass_index	0..1 String	Body mass index, calculated as weight/(height)squared	HumanVaginal
ethnicity	0..* String	A category of people who identify with each other, usually on the basis of pr...	HumanVaginal
host_occupation	0..1 String	Most frequent job performed by subject	HumanVaginal
medic_hist_perform	0..1 Boolean	Whether full medical history was collected	HumanVaginal
host_pulse	0..1 String	Resting pulse, measured as beats per minute	HumanVaginal
perturbation	0..* String	Type of perturbation, e	HumanVaginal
salinity	0..1 String	The total concentration of all dissolved salts in a liquid or solid sample	HumanVaginal
oxy_stat_samp	0..1 OXYSTATSAMPENUM	Oxygenation status of sample	HumanVaginal
organism_count	0..* String	Total cell count of any organism (or group of organisms) per gram, volume or ...	HumanVaginal
samp_store_temp	0..1 String	Temperature at which sample was stored, e	HumanVaginal
samp_store_loc	0..1 String	Location at which sample was stored, usually name of a specific freezer/room	HumanVaginal
samp_store_dur	0..1 String	Duration for which the sample was stored	HumanVaginal
host_symbiont	0..* String	The taxonomic name of the organism(s) found living in mutualistic, commensali...	HumanVaginal
misc_param	0..* String	Any other measurement performed or parameter collected, that is not listed he...	HumanVaginal

Usages

used by	used in	type	used
MixsCompliantData	mimag_human_vaginal_data	range	MimagHumanVaginal

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	MIXS:0010011_0016007
native	mixs_6_2_rc:MimagHumanVaginal

LinkML Source

Direct

name: MimagHumanVaginal
description: MIxS data that complies with the Mimag checklist and the HumanVaginal
  Extension
title: Mimag combined with HumanVaginal
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: HumanVaginal
mixins:
- Mimag
class_uri: MIXS:0010011_0016007

Induced

name: MimagHumanVaginal
description: MIxS data that complies with the Mimag checklist and the HumanVaginal
  Extension
title: Mimag combined with HumanVaginal
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: HumanVaginal
mixins:
- Mimag
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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    required: true
  bin_param:
    name: bin_param
    description: The parameters that have been applied during the extraction of genomes
      from metagenomic datasets
    title: binning parameters
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000077
    alias: bin_param
    owner: MimagHumanVaginal
    domain_of:
    - Mimag
    - Miuvig
    range: BIN_PARAM_ENUM
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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
  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: MimagHumanVaginal
    domain_of:
    - Mimag
    - Misag
    range: CONTAM_SCREEN_INPUT_ENUM
    required: false
    recommended: false
  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: MimagHumanVaginal
    domain_of:
    - Mimag
    - Misag
    - Miuvig
    range: COMPL_APPR_ENUM
    required: false
    recommended: false
  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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  bin_software:
    name: bin_software
    description: Tool(s) used for the extraction of genomes from metagenomic datasets,
      where possible include a product ID (PID) of the tool(s) used
    title: binning software
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{software};{version}{PID}'
    slot_uri: MIXS:0000078
    multivalued: false
    alias: bin_software
    owner: MimagHumanVaginal
    domain_of:
    - Mimag
    - Miuvig
    range: string
    required: true
  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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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
  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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
  lib_size:
    name: lib_size
    description: Total number of clones in the library prepared for the project
    title: library size
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000039
    multivalued: false
    alias: lib_size
    owner: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
  samp_mat_process:
    name: samp_mat_process
    description: A brief description of any processing applied to the sample during
      or after retrieving the sample from environment, or a link to the relevant protocol(s)
      performed
    title: sample material processing
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000016
    multivalued: false
    alias: samp_mat_process
    owner: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  mag_cov_software:
    name: mag_cov_software
    description: Tool(s) used to determine the genome coverage if coverage is used
      as a binning parameter in the extraction of genomes from metagenomic datasets
    title: MAG coverage software
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000080
    multivalued: false
    alias: mag_cov_software
    owner: MimagHumanVaginal
    domain_of:
    - Mimag
    - Miuvig
    range: MAG_COV_SOFTWARE_ENUM
    required: false
    recommended: false
  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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    domain_of:
    - Mimag
    - Misag
    range: string
    required: false
    recommended: false
  reassembly_bin:
    name: reassembly_bin
    description: Has an assembly been performed on a genome bin extracted from a metagenomic
      assembly?
    title: reassembly post binning
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000079
    multivalued: false
    alias: reassembly_bin
    owner: MimagHumanVaginal
    domain_of:
    - Mimag
    - Miuvig
    range: boolean
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  menarche:
    name: menarche
    description: Date of most recent menstruation
    title: menarche
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000965
    multivalued: false
    alias: menarche
    owner: MimagHumanVaginal
    domain_of:
    - HumanVaginal
    range: datetime
    required: false
    recommended: false
  sexual_act:
    name: sexual_act
    annotations:
      Expected_value:
        tag: Expected_value
        value: partner sex;frequency
    description: Current sexual partner and frequency of sex
    title: sexual activity
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000285
    multivalued: false
    alias: sexual_act
    owner: MimagHumanVaginal
    domain_of:
    - HumanVaginal
    range: string
    required: false
    recommended: false
  pregnancy:
    name: pregnancy
    description: Date due of pregnancy
    title: pregnancy
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000966
    multivalued: false
    alias: pregnancy
    owner: MimagHumanVaginal
    domain_of:
    - HumanVaginal
    range: datetime
    required: false
    recommended: false
  douche:
    name: douche
    description: Date of most recent douche
    title: douche
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000967
    multivalued: false
    alias: douche
    owner: MimagHumanVaginal
    domain_of:
    - HumanVaginal
    range: datetime
    required: false
    recommended: false
  birth_control:
    name: birth_control
    annotations:
      Expected_value:
        tag: Expected_value
        value: medication name
    description: Specification of birth control medication used
    title: birth control
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000286
    multivalued: false
    alias: birth_control
    owner: MimagHumanVaginal
    domain_of:
    - HumanVaginal
    range: string
    required: false
    recommended: false
  menopause:
    name: menopause
    description: Date of onset of menopause
    title: menopause
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000968
    multivalued: false
    alias: menopause
    owner: MimagHumanVaginal
    domain_of:
    - HumanVaginal
    range: datetime
    required: false
    recommended: false
  hrt:
    name: hrt
    description: Whether subject had hormone replacement theraphy, and if yes start
      date
    title: HRT
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000969
    multivalued: false
    alias: hrt
    owner: MimagHumanVaginal
    domain_of:
    - HumanVaginal
    range: datetime
    required: false
    recommended: false
  hysterectomy:
    name: hysterectomy
    description: Specification of whether hysterectomy was performed
    title: hysterectomy
    examples:
    - value: 'no'
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000287
    multivalued: false
    alias: hysterectomy
    owner: MimagHumanVaginal
    domain_of:
    - HumanVaginal
    range: boolean
    required: false
    recommended: false
  gynecologic_disord:
    name: gynecologic_disord
    description: History of gynecological disorders; can include multiple disorders.
      The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
      female reproductive system disease (https://disease-ontology.org/?id=DOID:229)
    title: gynecological disorder
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000288
    multivalued: true
    alias: gynecologic_disord
    owner: MimagHumanVaginal
    domain_of:
    - HumanVaginal
    range: string
    required: false
    recommended: false
  urogenit_disord:
    name: urogenit_disord
    description: History of urogenital disorders, can include multiple disorders.
      The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
      reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary
      system disease (https://disease-ontology.org/?id=DOID:18)
    title: urogenital disorder
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000289
    multivalued: true
    alias: urogenit_disord
    owner: MimagHumanVaginal
    domain_of:
    - HumanVaginal
    range: string
    required: false
    recommended: false
  host_subject_id:
    name: host_subject_id
    description: A unique identifier by which each subject can be referred to, de-identified
    title: host subject id
    examples:
    - value: MPI123
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000861
    multivalued: false
    alias: host_subject_id
    owner: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: Ectocervix [fma86484]
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000867
    multivalued: false
    alias: host_body_site
    owner: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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
  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: MimagHumanVaginal
    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
  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: MimagHumanVaginal
    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: MimagHumanVaginal
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
    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: MimagHumanVaginal
    domain_of:
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: boolean
    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: MimagHumanVaginal
    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
  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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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: MimagHumanVaginal
    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_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: MimagHumanVaginal
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  samp_store_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: MimagHumanVaginal
    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: MimagHumanVaginal
    domain_of:
    - Agriculture
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  misc_param:
    name: misc_param
    annotations:
      Expected_value:
        tag: Expected_value
        value: parameter name;measurement value
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    examples:
    - value: Bicarbonate ion concentration;2075 micromole per kilogram
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    multivalued: true
    alias: misc_param
    owner: MimagHumanVaginal
    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:0010011_0016007