Combination: Misag combined with HostAssociated (MisagHostAssociated)

MIxS Data that comply with the Misag checklist and the HostAssociated Extension

Composition

Misag [Checklist] + HostAssociated [Extension]

Terms

MIXS ID	Name	Cardinality and Range	Description
MIXS:0001107	samp_name	1 String	A local identifier or name that for the material sample used for extracting n...
MIXS:0000017	size_frac	0..1 String	Filtering pore size used in sample preparation
MIXS:0000043	lib_screen	0..1 recommended String	Specific enrichment or screening methods applied before and/or after creating...
MIXS:0000062	ref_db	0..1 String	List of database(s) used for ORF annotation, along with version number and re...
MIXS:0000038	nucl_acid_amp	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...
MIXS:0000039	lib_size	0..1 recommended Integer	Total number of clones in the library prepared for the project
MIXS:0000005	contam_screen_input	0..1 ContamScreenInputEnum	The type of sequence data used as input
MIXS:0000047	mid	0..1 recommended String	Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe...
MIXS:0000057	assembly_name	0..1 recommended String	Name/version of the assembly provided by the submitter that is used in the ge...
MIXS:0000113	temp	0..1 recommended String	Temperature of the sample at the time of sampling
MIXS:0000069	compl_score	1 String	Completeness score is typically based on either the fraction of markers found...
MIXS:0000067	trnas	0..1 String	The total number of tRNAs identified from the SAG or MAG
MIXS:0000037	nucl_acid_ext	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...
MIXS:0000001	samp_size	0..1 recommended String	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...
MIXS:0000094	alt	0..1 recommended String	Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba...
MIXS:0000026	source_mat_id	* recommended String	A unique identifier assigned to a material sample (as defined by http://rs
MIXS:0000111	samp_vol_we_dna_ext	0..1 String	Volume (ml) or mass (g) of total collected sample processed for DNA extractio...
MIXS:0000040	lib_reads_seqd	0..1 recommended Integer	Total number of clones sequenced from the library
MIXS:0000015	rel_to_oxygen	0..1 RelToOxygenEnum	Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ...
MIXS:0000006	wga_amp_kit	0..1 String	Kit used to amplify genomic DNA in preparation for sequencing
MIXS:0000074	decontam_software	0..1 String	Tool(s) used in contamination screening
MIXS:0000002	samp_collect_device	0..1 recommended String	The device used to collect an environmental sample
MIXS:0000060	number_contig	0..1 Integer	Total number of contigs in the cleaned/submitted assembly that makes up a giv...
MIXS:0000068	trna_ext_software	0..1 String	Tools used for tRNA identification
MIXS:0000054	sc_lysis_method	0..1 String	Name of the kit or standard protocol used for cell(s) or particle(s) lysis
MIXS:0000041	lib_layout	0..1 recommended LibLayoutEnum	Specify whether to expect single, paired, or other configuration of reads
MIXS:0000073	contam_screen_param	0..1 String	Specific parameters used in the decontamination sofware, such as reference da...
MIXS:0000056	assembly_qual	1 AssemblyQualEnum	The assembly quality category is based on sets of criteria outlined for each ...
MIXS:0000025	ref_biomaterial	0..1 String	Primary publication if isolated before genome publication; otherwise, primary...
MIXS:0000092	project_name	1 String	Name of the project within which the sequencing was organized
MIXS:0000042	lib_vector	0..1 recommended String	Cloning vector type(s) used in construction of libraries
MIXS:0000048	adapters	0..1 recommended String	Adapters provide priming sequences for both amplification and sequencing of t...
MIXS:0001321	neg_cont_type	0..1 recommended NegContTypeEnum	The substance or equipment used as a negative control in an investigation
MIXS:0000058	assembly_software	1 String	Tool(s) used for assembly, including version number and parameters
MIXS:0000053	tax_ident	1 TaxIdentEnum	The phylogenetic marker(s) used to assign an organism name to the SAG or MAG
MIXS:0000072	contam_score	1 Float	The contamination score is based on the fraction of single-copy genes that ar...
MIXS:0000059	annot	0..1 String	Tool used for annotation, or for cases where annotation was provided by a com...
MIXS:0000066	x16s_recover_software	0..1 String	Tools used for 16S rRNA gene extraction
MIXS:0000065	x16s_recover	0..1 Boolean	Can a 16S gene be recovered from the submitted SAG or MAG?
MIXS:0001322	pos_cont_type	0..1 recommended String	The substance, mixture, product, or apparatus used to verify that a process w...
MIXS:0000061	feat_pred	0..1 String	Method used to predict UViGs features such as ORFs, integration site, etc
MIXS:0000070	compl_software	1 String	Tools used for completion estimate, i
MIXS:0000013	env_local_scale	1 String	Report the entity or entities which are in the sample or specimen s local vic...
MIXS:0000075	sort_tech	1 SortTechEnum	Method used to sort/isolate cells or particles of interest
MIXS:0000016	samp_mat_process	0..1 recommended String	A brief description of any processing applied to the sample during or after r...
MIXS:0000063	sim_search_meth	0..1 String	Tool used to compare ORFs with database, along with version and cutoffs used
MIXS:0000018	depth	0..1 recommended String	The vertical distance below local surface
MIXS:0001225	samp_collect_method	0..1 recommended String	The method employed for collecting the sample
MIXS:0000055	wga_amp_appr	1 WgaAmpApprEnum	Method used to amplify genomic DNA in preparation for sequencing
MIXS:0000071	compl_appr	0..1 ComplApprEnum	The approach used to determine the completeness of a given genomic assembly, ...
MIXS:0000014	env_medium	1 String	Report the environmental material(s) immediately surrounding the sample or sp...
MIXS:0001320	samp_taxon_id	1 String	NCBI taxon id of the sample
MIXS:0000010	geo_loc_name	1 String	The geographical origin of the sample as defined by the country or sea name f...
MIXS:0000076	sc_lysis_approach	1 ScLysisApproachEnum	Method used to free DNA from interior of the cell(s) or particle(s)
MIXS:0000011	collection_date	1 Datetime	The time of sampling, either as an instance (single point in time) or interva...
MIXS:0000050	seq_meth	1 String	Sequencing machine used
MIXS:0000009	lat_lon	1 String	The geographical origin of the sample as defined by latitude and longitude
MIXS:0000093	elev	0..1 recommended String	Elevation of the sampling site is its height above a fixed reference point, m...
MIXS:0000012	env_broad_scale	1 String	Report the major environmental system the sample or specimen came from
MIXS:0000064	tax_class	0..1 String	Method used for taxonomic classification, along with reference database used,...
MIXS:0000008	experimental_factor	* recommended String	Variable aspects of an experiment design that can be used to describe an expe...
MIXS:0000091	associated_resource	* recommended String	A related resource that is referenced, cited, or otherwise associated to the ...
MIXS:0000090	sop	* recommended String	Standard operating procedures used in assembly and/or annotation of genomes, ...
MIXS:0000247	ances_data	0..1 String	Information about either pedigree or other ancestral information description ...
MIXS:0000858	biol_stat	0..1 BiolStatEnum	The level of genome modification
MIXS:0000859	genetic_mod	0..1 String	Genetic modifications of the genome of an organism, which may occur naturally...
MIXS:0000248	host_common_name	0..1 String	Common name of the host
MIXS:0000860	samp_capt_status	0..1 SampCaptStatusEnum	Reason for the sample
MIXS:0000249	samp_dis_stage	0..1 SampDisStageEnum	Stage of the disease at the time of sample collection, e
MIXS:0000250	host_taxid	0..1 String	NCBI taxon id of the host, e
MIXS:0000861	host_subject_id	0..1 String	A unique identifier by which each subject can be referred to, de-identified
MIXS:0000255	host_age	0..1 String	Age of host at the time of sampling; relevant scale depends on species and st...
MIXS:0000251	host_life_stage	0..1 String	Description of life stage of host
MIXS:0000811	host_sex	0..1 String	Gender or physical sex of the host
MIXS:0000031	host_disease_stat	0..1 String	List of diseases with which the host has been diagnosed; can include multiple...
MIXS:0000751	chem_administration	* String	List of chemical compounds administered to the host or site where sampling oc...
MIXS:0000866	host_body_habitat	0..1 String	Original body habitat where the sample was obtained from
MIXS:0000867	host_body_site	0..1 String	Name of body site where the sample was obtained from, such as a specific orga...
MIXS:0000888	host_body_product	0..1 String	Substance produced by the body, e
MIXS:0000263	host_tot_mass	0..1 String	Total mass of the host at collection, the unit depends on host
MIXS:0000264	host_height	0..1 String	The height of subject
MIXS:0000256	host_length	0..1 String	The length of subject
MIXS:0000869	host_diet	* String	Type of diet depending on the host, for animals omnivore, herbivore etc
MIXS:0000870	host_last_meal	* String	Content of last meal and time since feeding; can include multiple values
MIXS:0000871	host_growth_cond	0..1 String	Literature reference giving growth conditions of the host
MIXS:0000252	host_substrate	0..1 String	The growth substrate of the host
MIXS:0000872	host_fam_rel	* String	Relationships to other hosts in the same study; can include multiple relation...
MIXS:0001318	host_subspecf_genlin	* String	Information about the genetic distinctness of the host organism below the sub...
MIXS:0000365	host_genotype	0..1 String	Observed genotype
MIXS:0000874	host_phenotype	0..1 String	Phenotype of human or other host
MIXS:0000274	host_body_temp	0..1 String	Core body temperature of the host when sample was collected
MIXS:0000257	host_dry_mass	0..1 String	Measurement of dry mass
MIXS:0000258	blood_press_diast	0..1 String	Resting diastolic blood pressure, measured as mm mercury
MIXS:0000259	blood_press_syst	0..1 String	Resting systolic blood pressure, measured as mm mercury
MIXS:0000260	host_color	0..1 String	The color of host
MIXS:0000261	host_shape	0..1 String	Morphological shape of host
MIXS:0000875	gravidity	0..1 String	Whether or not subject is gravid, and if yes date due or date post-conception...
MIXS:0000754	perturbation	* String	Type of perturbation, e
MIXS:0000183	salinity	0..1 String	The total concentration of all dissolved salts in a liquid or solid sample
MIXS:0000753	oxy_stat_samp	0..1 OxyStatSampEnum	Oxygenation status of sample
MIXS:0000103	organism_count	* String	Total cell count of any organism (or group of organisms) per gram, volume or ...
MIXS:0000110	samp_store_temp	0..1 String	Temperature at which sample was stored, e
MIXS:0000116	samp_store_dur	0..1 String	Duration for which the sample was stored
MIXS:0000755	samp_store_loc	0..1 String	Location at which sample was stored, usually name of a specific freezer/room
MIXS:0001298	host_symbiont	* String	The taxonomic name of the organism(s) found living in mutualistic, commensali...
MIXS:0000752	misc_param	* String	Any other measurement performed or parameter collected, that is not listed he...

LinkML Source

Direct

name: MisagHostAssociated
description: MIxS Data that comply with the Misag checklist and the HostAssociated
  Extension
title: Misag combined with HostAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: HostAssociated
mixins:
- Misag
class_uri: MIXS:0010010_0016002

Induced

name: MisagHostAssociated
description: MIxS Data that comply with the Misag checklist and the HostAssociated
  Extension
title: Misag combined with HostAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: HostAssociated
mixins:
- Misag
attributes:
  samp_name:
    name: samp_name
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ''
    description: A local identifier or name that for the material sample used for
      extracting nucleic acids, and subsequent sequencing. It can refer either to
      the original material collected or to any derived sub-samples. It can have any
      format, but we suggest that you make it concise, unique and consistent within
      your lab, and as informative as possible. INSDC requires every sample name from
      a single Submitter to be unique. Use of a globally unique identifier for the
      field source_mat_id is recommended in addition to sample_name
    title: sample name
    examples:
    - value: ISDsoil1
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    slot_uri: MIXS:0001107
    alias: samp_name
    owner: MisagHostAssociated
    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
  size_frac:
    name: size_frac
    annotations:
      Expected_value:
        tag: Expected_value
        value: filter size value range
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    examples:
    - value: 0-0.22 micrometer
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - fraction
    - size
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    alias: size_frac
    owner: MisagHostAssociated
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
  lib_screen:
    name: lib_screen
    annotations:
      Expected_value:
        tag: Expected_value
        value: screening strategy name
    description: Specific enrichment or screening methods applied before and/or after
      creating libraries
    title: library screening strategy
    examples:
    - value: enriched, screened, normalized
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000043
    alias: lib_screen
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  ref_db:
    name: ref_db
    annotations:
      Expected_value:
        tag: Expected_value
        value: names, versions, and references of databases
    description: List of database(s) used for ORF annotation, along with version number
      and reference to website or publication
    title: reference database(s)
    examples:
    - value: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017
        doi:10.1093/nar/gkw975
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - database
    string_serialization: '{database};{version};{reference}'
    slot_uri: MIXS:0000062
    alias: ref_db
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
  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
    examples:
    - value: https://phylogenomics.me/protocols/16s-pcr-protocol/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000038
    alias: nucl_acid_amp
    owner: MisagHostAssociated
    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_size:
    name: lib_size
    description: Total number of clones in the library prepared for the project
    title: library size
    examples:
    - value: '50'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    - size
    slot_uri: MIXS:0000039
    alias: lib_size
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    recommended: true
  contam_screen_input:
    name: contam_screen_input
    description: The type of sequence data used as input
    title: contamination screening input
    examples:
    - value: contigs
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000005
    alias: contam_screen_input
    owner: MisagHostAssociated
    domain_of:
    - Mimag
    - Misag
    range: ContamScreenInputEnum
  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
    examples:
    - value: GTGAATAT
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - identifier
    slot_uri: MIXS:0000047
    alias: mid
    owner: MisagHostAssociated
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^[ACGTRKSYMWBHDVN]+$
    structured_pattern:
      syntax: ^{ambiguous_nucleotides}$
      interpolated: true
      partial_match: true
  assembly_name:
    name: assembly_name
    annotations:
      Expected_value:
        tag: Expected_value
        value: name and version of assembly
    description: Name/version of the assembly provided by the submitter that is used
      in the genome browsers and in the community
    title: assembly name
    examples:
    - value: HuRef, JCVI_ISG_i3_1.0
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    string_serialization: '{text} {text}'
    slot_uri: MIXS:0000057
    alias: assembly_name
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  temp:
    name: temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature of the sample at the time of sampling
    title: temperature
    examples:
    - value: 25 degree Celsius
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - temperature
    slot_uri: MIXS:0000113
    alias: temp
    owner: MisagHostAssociated
    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
    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
  compl_score:
    name: compl_score
    annotations:
      Expected_value:
        tag: Expected_value
        value: quality;percent completeness
    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
    examples:
    - value: med;60%
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - score
    string_serialization: '[high|med|low];{percentage}'
    slot_uri: MIXS:0000069
    alias: compl_score
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: string
    required: true
  trnas:
    name: trnas
    annotations:
      Expected_value:
        tag: Expected_value
        value: value from 0-21
    description: The total number of tRNAs identified from the SAG or MAG
    title: number of standard tRNAs extracted
    examples:
    - value: '18'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - number
    string_serialization: '{integer}'
    slot_uri: MIXS:0000067
    alias: trnas
    owner: MisagHostAssociated
    domain_of:
    - Mimag
    - Misag
    - Miuvig
    range: string
  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
    examples:
    - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000037
    alias: nucl_acid_ext
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  samp_size:
    name: samp_size
    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
      sample collected
    title: amount or size of sample collected
    examples:
    - value: 5 liter
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - size
    slot_uri: MIXS:0000001
    alias: samp_size
    owner: MisagHostAssociated
    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
  alt:
    name: alt
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    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
    examples:
    - value: 100 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000094
    alias: alt
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - HostAssociated
    - MiscellaneousNaturalOrArtificialEnvironment
    - SymbiontAssociated
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  source_mat_id:
    name: source_mat_id
    annotations:
      Expected_value:
        tag: Expected_value
        value: 'for cultures of microorganisms: identifiers for two culture collections;
          for other material a unique arbitrary identifer'
    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
    examples:
    - value: MPI012345
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - identifier
    - material
    - source
    slot_uri: MIXS:0000026
    alias: source_mat_id
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - SymbiontAssociated
    range: string
    recommended: true
    multivalued: true
  samp_vol_we_dna_ext:
    name: samp_vol_we_dna_ext
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milliliter, gram, milligram, square centimeter
    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
    examples:
    - value: 1500 milliliter
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - dna
    - sample
    - volume
    - weight
    slot_uri: MIXS:0000111
    alias: samp_vol_we_dna_ext
    owner: MisagHostAssociated
    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
    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
  lib_reads_seqd:
    name: lib_reads_seqd
    description: Total number of clones sequenced from the library
    title: library reads sequenced
    examples:
    - value: '20'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000040
    alias: lib_reads_seqd
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    recommended: true
  rel_to_oxygen:
    name: rel_to_oxygen
    description: Is this organism an aerobe, anaerobe? Please note that aerobic and
      anaerobic are valid descriptors for microbial environments
    title: relationship to oxygen
    examples:
    - value: aerobe
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - oxygen
    - relationship
    slot_uri: MIXS:0000015
    alias: rel_to_oxygen
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    range: RelToOxygenEnum
  wga_amp_kit:
    name: wga_amp_kit
    annotations:
      Expected_value:
        tag: Expected_value
        value: kit name
    description: Kit used to amplify genomic DNA in preparation for sequencing
    title: WGA amplification kit
    examples:
    - value: qiagen repli-g
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - kit
    slot_uri: MIXS:0000006
    alias: wga_amp_kit
    owner: MisagHostAssociated
    domain_of:
    - Misag
    - Miuvig
    range: string
  decontam_software:
    name: decontam_software
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration
    description: Tool(s) used in contamination screening
    title: decontamination software
    examples:
    - value: anvi'o
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    string_serialization: '[checkm/refinem|anvi''o|prodege|bbtools:decontaminate.sh|acdc|combination]'
    slot_uri: MIXS:0000074
    alias: decontam_software
    owner: MisagHostAssociated
    domain_of:
    - Mimag
    - Misag
    range: string
  samp_collect_device:
    name: samp_collect_device
    annotations:
      Expected_value:
        tag: Expected_value
        value: device name
    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]
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - device
    - sample
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000002
    alias: samp_collect_device
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: 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
    examples:
    - value: '40'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - number
    slot_uri: MIXS:0000060
    alias: number_contig
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: integer
  trna_ext_software:
    name: trna_ext_software
    description: Tools used for tRNA identification
    title: tRNA extraction software
    examples:
    - value: infernal;v2;default parameters
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    slot_uri: MIXS:0000068
    alias: trna_ext_software
    owner: MisagHostAssociated
    domain_of:
    - Mimag
    - Misag
    - Miuvig
    range: string
    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
  sc_lysis_method:
    name: sc_lysis_method
    annotations:
      Expected_value:
        tag: Expected_value
        value: kit, protocol name
    description: Name of the kit or standard protocol used for cell(s) or particle(s)
      lysis
    title: single cell or viral particle lysis kit protocol
    examples:
    - value: ambion single cell lysis kit
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - kit
    - particle
    - protocol
    - single
    slot_uri: MIXS:0000054
    alias: sc_lysis_method
    owner: MisagHostAssociated
    domain_of:
    - Misag
    - Miuvig
    range: string
  lib_layout:
    name: lib_layout
    description: Specify whether to expect single, paired, or other configuration
      of reads
    title: library layout
    examples:
    - value: paired
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000041
    alias: lib_layout
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: LibLayoutEnum
    recommended: true
  contam_screen_param:
    name: contam_screen_param
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration;value or name
    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
    examples:
    - value: kmer
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - parameter
    string_serialization: '[ref db|kmer|coverage|combination];{text|integer}'
    slot_uri: MIXS:0000073
    alias: contam_screen_param
    owner: MisagHostAssociated
    domain_of:
    - Mimag
    - Misag
    range: string
  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 large subunit (LSU) RNA,
      small subunit (SSU) and the presence of 5.8S rRNA or 5S rRNA depending on whether
      it is a eukaryotic or prokaryotic genome, respectively. 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
    examples:
    - value: High-quality draft genome
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - quality
    slot_uri: MIXS:0000056
    alias: assembly_qual
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: AssemblyQualEnum
    required: true
  ref_biomaterial:
    name: ref_biomaterial
    description: Primary publication if isolated before genome publication; otherwise,
      primary genome report
    title: reference for biomaterial
    examples:
    - value: doi:10.1016/j.syapm.2018.01.009
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000025
    alias: ref_biomaterial
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    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
  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
    keywords:
    - project
    slot_uri: MIXS:0000092
    alias: project_name
    owner: MisagHostAssociated
    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
  lib_vector:
    name: lib_vector
    annotations:
      Expected_value:
        tag: Expected_value
        value: vector
    description: Cloning vector type(s) used in construction of libraries
    title: library vector
    examples:
    - value: Bacteriophage P1
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000042
    alias: lib_vector
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - 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
    examples:
    - value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000048
    alias: adapters
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    structured_pattern:
      syntax: ^{adapter_A_DNA_sequence};{adapter_B_DNA_sequence}$
      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
    keywords:
    - type
    slot_uri: MIXS:0001321
    alias: neg_cont_type
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: NegContTypeEnum
    recommended: true
  assembly_software:
    name: assembly_software
    description: Tool(s) used for assembly, including version number and parameters
    title: assembly software
    examples:
    - value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    slot_uri: MIXS:0000058
    alias: assembly_software
    owner: MisagHostAssociated
    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
  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
    examples:
    - value: other
      description: was other <colon> rpoB gene
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - identifier
    - marker
    - taxon
    slot_uri: MIXS:0000053
    alias: tax_ident
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: TaxIdentEnum
    required: 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
    examples:
    - value: '0.01'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - score
    slot_uri: MIXS:0000072
    alias: contam_score
    owner: MisagHostAssociated
    domain_of:
    - Mimag
    - Misag
    range: float
    required: true
  annot:
    name: annot
    annotations:
      Expected_value:
        tag: Expected_value
        value: name of tool or pipeline used, or annotation source description
    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
    examples:
    - value: prokka
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000059
    alias: annot
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
  x16s_recover_software:
    name: x16s_recover_software
    description: Tools used for 16S rRNA gene extraction
    title: 16S recovery software
    examples:
    - value: rambl;v2;default parameters
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - recover
    - software
    slot_uri: MIXS:0000066
    alias: x16s_recover_software
    owner: MisagHostAssociated
    domain_of:
    - Mimag
    - Misag
    range: string
    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
  x16s_recover:
    name: x16s_recover
    description: Can a 16S gene be recovered from the submitted SAG or MAG?
    title: 16S recovered
    examples:
    - value: 'yes'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - recover
    slot_uri: MIXS:0000065
    alias: x16s_recover
    owner: MisagHostAssociated
    domain_of:
    - Mimag
    - Misag
    range: boolean
  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
    keywords:
    - type
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    alias: pos_cont_type
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    recommended: true
  feat_pred:
    name: feat_pred
    description: Method used to predict UViGs features such as ORFs, integration site,
      etc
    title: feature prediction
    examples:
    - value: Prodigal;2.6.3;default parameters
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - feature
    - predict
    slot_uri: MIXS:0000061
    alias: feat_pred
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    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
  compl_software:
    name: compl_software
    annotations:
      Expected_value:
        tag: Expected_value
        value: names and versions of software(s) used
    description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
    title: completeness software
    examples:
    - value: checkm
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    string_serialization: '{software};{version}'
    slot_uri: MIXS:0000070
    alias: compl_software
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: string
    required: 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
    keywords:
    - context
    - environmental
    slot_uri: MIXS:0000013
    alias: env_local_scale
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  sort_tech:
    name: sort_tech
    description: Method used to sort/isolate cells or particles of interest
    title: sorting technology
    examples:
    - value: optical manipulation
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000075
    alias: sort_tech
    owner: MisagHostAssociated
    domain_of:
    - Misag
    - Miuvig
    range: SortTechEnum
    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
    examples:
    - value: filtering of seawater, storing samples in ethanol
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - material
    - process
    - sample
    slot_uri: MIXS:0000016
    alias: samp_mat_process
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: 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
    examples:
    - value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    slot_uri: MIXS:0000063
    alias: sim_search_meth
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    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
  depth:
    name: depth
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    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
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - depth
    slot_uri: MIXS:0000018
    alias: depth
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_collect_method:
    name: samp_collect_method
    description: The method employed for collecting the sample
    title: sample collection method
    examples:
    - value: swabbing
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    - sample
    slot_uri: MIXS:0001225
    alias: samp_collect_method
    owner: MisagHostAssociated
    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
  wga_amp_appr:
    name: wga_amp_appr
    description: Method used to amplify genomic DNA in preparation for sequencing
    title: WGA amplification approach
    examples:
    - value: mda based
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000055
    alias: wga_amp_appr
    owner: MisagHostAssociated
    domain_of:
    - Misag
    - Miuvig
    range: WgaAmpApprEnum
    required: true
  compl_appr:
    name: compl_appr
    annotations:
      Expected_value:
        tag: Expected_value
        value: text
    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
    examples:
    - value: other
      description: was other <colon> UViG length compared to the average length of
        reference genomes from the P22virus genus (NCBI RefSeq v83)
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000071
    alias: compl_appr
    owner: MisagHostAssociated
    domain_of:
    - Mimag
    - Misag
    - Miuvig
    range: ComplApprEnum
  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
    keywords:
    - environmental
    slot_uri: MIXS:0000014
    alias: env_medium
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  samp_taxon_id:
    name: samp_taxon_id
    description: NCBI taxon id of the sample.  Maybe be a single taxon or mixed taxa
      sample. Use 'synthetic metagenome  for mock community/positive controls, or
      'blank sample' for negative controls
    title: taxonomy ID of DNA sample
    examples:
    - value: Gut Metagenome [NCBITaxon:749906]
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - dna
    - identifier
    - sample
    - taxon
    slot_uri: MIXS:0001320
    alias: samp_taxon_id
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$
    structured_pattern:
      syntax: ^{text} \[{NCBItaxon_id}\]$
      interpolated: true
      partial_match: true
  geo_loc_name:
    name: geo_loc_name
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name. Country or sea names should be chosen
      from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
      (http://purl.bioontology.org/ontology/GAZ)
    title: geographic location (country and/or sea,region)
    examples:
    - value: 'USA: Maryland, Bethesda'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - geographic
    - location
    slot_uri: MIXS:0000010
    alias: geo_loc_name
    owner: MisagHostAssociated
    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
  sc_lysis_approach:
    name: sc_lysis_approach
    description: Method used to free DNA from interior of the cell(s) or particle(s)
    title: single cell or viral particle lysis approach
    examples:
    - value: enzymatic
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - particle
    - single
    slot_uri: MIXS:0000076
    alias: sc_lysis_approach
    owner: MisagHostAssociated
    domain_of:
    - Misag
    - Miuvig
    range: ScLysisApproachEnum
    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
    keywords:
    - date
    slot_uri: MIXS:0000011
    alias: collection_date
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: datetime
    required: true
  seq_meth:
    name: seq_meth
    description: Sequencing machine used. Where possible the term should be taken
      from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)
    title: sequencing method
    examples:
    - value: 454 Genome Sequencer FLX [OBI:0000702]
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    slot_uri: MIXS:0000050
    alias: seq_meth
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
    structured_pattern:
      syntax: ^{text}|({termLabel} \[{termID}\])$
      interpolated: true
      partial_match: true
  lat_lon:
    name: lat_lon
    description: The geographical origin of the sample as defined by latitude and
      longitude. The values should be reported in decimal degrees, limited to 8 decimal
      points, 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
    keywords:
    - geographic
    - location
    slot_uri: MIXS:0000009
    alias: lat_lon
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: string
    required: true
    pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$
    structured_pattern:
      syntax: ^{lat} {lon}$
      interpolated: true
      partial_match: true
  elev:
    name: elev
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit
    title: elevation
    examples:
    - value: 100 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - elevation
    slot_uri: MIXS:0000093
    alias: elev
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - HostAssociated
    - HydrocarbonResourcesCores
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - Water
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  env_broad_scale:
    name: env_broad_scale
    description: 'Report the major environmental system the sample or specimen came
      from. The system(s) identified should have a coarse spatial grain, to provide
      the general environmental context of where the sampling was done (e.g. in the
      desert or a rainforest). We recommend using subclasses of EnvO s biome class:  http://purl.obolibrary.org/obo/ENVO_00000428.
      EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: broad-scale environmental context
    examples:
    - value: rangeland biome [ENVO:01000247]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - context
    - environmental
    slot_uri: MIXS:0000012
    alias: env_broad_scale
    owner: MisagHostAssociated
    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
  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
    examples:
    - value: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification,
        default parameters)
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - classification
    - taxon
    slot_uri: MIXS:0000064
    alias: tax_class
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
  experimental_factor:
    name: experimental_factor
    annotations:
      Expected_value:
        tag: Expected_value
        value: text or EFO and/or OBI
    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
    examples:
    - value: time series design [EFO:0001779]
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - experimental
    - factor
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000008
    alias: experimental_factor
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    multivalued: true
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  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
    keywords:
    - resource
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000091
    alias: associated_resource
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    multivalued: true
  sop:
    name: sop
    annotations:
      Expected_value:
        tag: Expected_value
        value: reference to SOP
    description: Standard operating procedures used in assembly and/or annotation
      of genomes, metagenomes or environmental sequences
    title: relevant standard operating procedures
    examples:
    - value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - procedures
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000090
    alias: sop
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    multivalued: true
  ances_data:
    name: ances_data
    description: Information about either pedigree or other ancestral information
      description (e.g. parental variety in case of mutant or selection), e.g. A/3*B
      (meaning [(A x B) x B] x B)
    title: ancestral data
    examples:
    - value: A/3*B
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000247
    alias: ances_data
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    range: string
  biol_stat:
    name: biol_stat
    description: The level of genome modification
    title: biological status
    examples:
    - value: natural
    from_schema: https://w3id.org/mixs
    keywords:
    - status
    slot_uri: MIXS:0000858
    alias: biol_stat
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - PlantAssociated
    range: BiolStatEnum
  genetic_mod:
    name: genetic_mod
    annotations:
      Expected_value:
        tag: Expected_value
        value: PMID, DOI, URL or text
    description: Genetic modifications of the genome of an organism, which may occur
      naturally by spontaneous mutation, or be introduced by some experimental means,
      e.g. specification of a transgene or the gene knocked-out or details of transient
      transfection
    title: genetic modification
    examples:
    - value: aox1A transgenic
    from_schema: https://w3id.org/mixs
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000859
    alias: genetic_mod
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - PlantAssociated
    range: string
  host_common_name:
    name: host_common_name
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ''
    description: Common name of the host
    title: host common name
    examples:
    - value: human
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000248
    alias: host_common_name
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
  samp_capt_status:
    name: samp_capt_status
    description: Reason for the sample
    title: sample capture status
    examples:
    - value: farm sample
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - status
    slot_uri: MIXS:0000860
    alias: samp_capt_status
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - PlantAssociated
    range: SampCaptStatusEnum
  samp_dis_stage:
    name: samp_dis_stage
    description: Stage of the disease at the time of sample collection, e.g. inoculation,
      penetration, infection, growth and reproduction, dissemination of pathogen
    title: sample disease stage
    examples:
    - value: infection
    from_schema: https://w3id.org/mixs
    keywords:
    - disease
    - sample
    slot_uri: MIXS:0000249
    alias: samp_dis_stage
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - PlantAssociated
    range: SampDisStageEnum
  host_taxid:
    name: host_taxid
    annotations:
      Expected_value:
        tag: Expected_value
        value: NCBI taxon identifier
    description: NCBI taxon id of the host, e.g. 9606
    title: host taxid
    examples:
    - value: '7955'
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - taxon
    string_serialization: '{NCBI taxid}'
    slot_uri: MIXS:0000250
    alias: host_taxid
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
  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
    keywords:
    - host
    - host.
    - identifier
    slot_uri: MIXS:0000861
    alias: host_subject_id
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
  host_age:
    name: host_age
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: year, day, hour
    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: 10 days
    from_schema: https://w3id.org/mixs
    keywords:
    - age
    - host
    - host.
    slot_uri: MIXS:0000255
    alias: host_age
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    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_life_stage:
    name: host_life_stage
    annotations:
      Expected_value:
        tag: Expected_value
        value: stage
    description: Description of life stage of host
    title: host life stage
    examples:
    - value: adult
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - life
    slot_uri: MIXS:0000251
    alias: host_life_stage
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
  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
    keywords:
    - host
    - host.
    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: MisagHostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
  host_disease_stat:
    name: host_disease_stat
    annotations:
      Expected_value:
        tag: Expected_value
        value: disease name or Disease Ontology term
    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: rabies [DOID:11260]
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - disease
    - host
    - host.
    - status
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000031
    alias: host_disease_stat
    owner: MisagHostAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    range: string
  chem_administration:
    name: chem_administration
    annotations:
      Expected_value:
        tag: Expected_value
        value: CHEBI;timestamp
    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
    examples:
    - value: agar [CHEBI:2509];2018-05-11T20:00Z
    from_schema: https://w3id.org/mixs
    keywords:
    - administration
    string_serialization: '{termLabel} [{termID}];{timestamp}'
    slot_uri: MIXS:0000751
    alias: chem_administration
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  host_body_habitat:
    name: host_body_habitat
    description: Original body habitat where the sample was obtained from
    title: host body habitat
    examples:
    - value: nasopharynx
    from_schema: https://w3id.org/mixs
    keywords:
    - body
    - habitat
    - host
    - host.
    slot_uri: MIXS:0000866
    alias: host_body_habitat
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  host_body_site:
    name: host_body_site
    annotations:
      Expected_value:
        tag: Expected_value
        value: FMA or UBERON
    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: gill [UBERON:0002535]
    from_schema: https://w3id.org/mixs
    keywords:
    - body
    - host
    - site
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000867
    alias: host_body_site
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
  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
    keywords:
    - body
    - host
    - host.
    - product
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000888
    alias: host_body_product
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
  host_tot_mass:
    name: host_tot_mass
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: kilogram, gram
    description: Total mass of the host at collection, the unit depends on host
    title: host total mass
    examples:
    - value: 2500 gram
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - mass
    - total
    slot_uri: MIXS:0000263
    alias: host_tot_mass
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    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
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: centimeter, millimeter, meter
    description: The height of subject
    title: host height
    examples:
    - value: 0.1 meter
    from_schema: https://w3id.org/mixs
    keywords:
    - height
    - host
    - host.
    slot_uri: MIXS:0000264
    alias: host_height
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_length:
    name: host_length
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: centimeter, millimeter, meter
    description: The length of subject
    title: host length
    examples:
    - value: 1 meter
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - length
    slot_uri: MIXS:0000256
    alias: host_length
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    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: herbivore
    from_schema: https://w3id.org/mixs
    keywords:
    - diet
    - host
    - host.
    slot_uri: MIXS:0000869
    alias: host_diet
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
    multivalued: true
  host_last_meal:
    name: host_last_meal
    annotations:
      Expected_value:
        tag: Expected_value
        value: content;duration
    description: Content of last meal and time since feeding; can include multiple
      values
    title: host last meal
    examples:
    - value: corn feed;P2H
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    string_serialization: '{text};{duration}'
    slot_uri: MIXS:0000870
    alias: host_last_meal
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
    multivalued: true
  host_growth_cond:
    name: host_growth_cond
    description: Literature reference giving growth conditions of the host
    title: host growth conditions
    examples:
    - value: https://academic.oup.com/icesjms/article/68/2/349/617247
    from_schema: https://w3id.org/mixs
    keywords:
    - condition
    - growth
    - host
    - host.
    slot_uri: MIXS:0000871
    alias: host_growth_cond
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: true
  host_substrate:
    name: host_substrate
    description: The growth substrate of the host
    title: host substrate
    examples:
    - value: rock
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000252
    alias: host_substrate
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  host_fam_rel:
    name: host_fam_rel
    annotations:
      Expected_value:
        tag: Expected_value
        value: relationship type;arbitrary identifier
    description: Relationships to other hosts in the same study; can include multiple
      relationships
    title: host family relationship
    examples:
    - value: offspring;Mussel25
    from_schema: https://w3id.org/mixs
    keywords:
    - family
    - host
    - host.
    - relationship
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0000872
    alias: host_fam_rel
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - SymbiontAssociated
    range: string
    multivalued: true
  host_subspecf_genlin:
    name: host_subspecf_genlin
    annotations:
      Expected_value:
        tag: Expected_value
        value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,
          e.g. serovar, biotype, ecotype, variety, cultivar
    description: Information about the genetic distinctness of the host organism below
      the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,
      or any relevant genetic typing schemes like Group I plasmid. Subspecies should
      not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage
      name and the lineage rank separated by a colon, e.g., biovar:abc123
    title: host subspecific genetic lineage
    examples:
    - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - lineage
    string_serialization: '{rank name}:{text}'
    slot_uri: MIXS:0001318
    alias: host_subspecf_genlin
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    range: string
    multivalued: true
  host_genotype:
    name: host_genotype
    description: Observed genotype
    title: host genotype
    examples:
    - value: C57BL/6
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000365
    alias: host_genotype
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
  host_phenotype:
    name: host_phenotype
    annotations:
      Expected_value:
        tag: Expected_value
        value: PATO or HP
    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: elongated [PATO:0001154]
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000874
    alias: host_phenotype
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
  host_body_temp:
    name: host_body_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Core body temperature of the host when sample was collected
    title: host body temperature
    examples:
    - value: 15 degree Celsius
    from_schema: https://w3id.org/mixs
    keywords:
    - body
    - host
    - host.
    - temperature
    slot_uri: MIXS:0000274
    alias: host_body_temp
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    range: string
    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_dry_mass:
    name: host_dry_mass
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: kilogram, gram
    description: Measurement of dry mass
    title: host dry mass
    examples:
    - value: 500 gram
    from_schema: https://w3id.org/mixs
    keywords:
    - dry
    - host
    - host.
    - mass
    slot_uri: MIXS:0000257
    alias: host_dry_mass
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    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
  blood_press_diast:
    name: blood_press_diast
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: millimeter mercury
    description: Resting diastolic blood pressure, measured as mm mercury
    title: host blood pressure diastolic
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - pressure
    slot_uri: MIXS:0000258
    alias: blood_press_diast
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    range: string
    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
  blood_press_syst:
    name: blood_press_syst
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: millimeter mercury
    description: Resting systolic blood pressure, measured as mm mercury
    title: host blood pressure systolic
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - pressure
    slot_uri: MIXS:0000259
    alias: blood_press_syst
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_color:
    name: host_color
    description: The color of host
    title: host color
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000260
    alias: host_color
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  host_shape:
    name: host_shape
    description: Morphological shape of host
    title: host shape
    examples:
    - value: round
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000261
    alias: host_shape
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  gravidity:
    name: gravidity
    description: Whether or not subject is gravid, and if yes date due or date post-conception,
      specifying which is used
    title: gravidity
    examples:
    - value: yes;due date:2018-05-11
    from_schema: https://w3id.org/mixs
    string_serialization: '{boolean};{timestamp}'
    slot_uri: MIXS:0000875
    alias: gravidity
    owner: MisagHostAssociated
    domain_of:
    - HostAssociated
    - SymbiontAssociated
    range: string
  perturbation:
    name: perturbation
    annotations:
      Expected_value:
        tag: Expected_value
        value: perturbation type name;perturbation interval and duration
    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
    examples:
    - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - perturbation
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000754
    alias: perturbation
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  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
    keywords:
    - salinity
    slot_uri: MIXS:0000183
    alias: salinity
    owner: MisagHostAssociated
    domain_of:
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    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
    examples:
    - value: aerobic
    from_schema: https://w3id.org/mixs
    keywords:
    - oxygen
    - sample
    - status
    slot_uri: MIXS:0000753
    alias: oxy_stat_samp
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - Air
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: OxyStatSampEnum
  organism_count:
    name: organism_count
    annotations:
      Expected_value:
        tag: Expected_value
        value: organism name;measurement value;enumeration
    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
    keywords:
    - count
    - organism
    string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
    slot_uri: MIXS:0000103
    alias: organism_count
    owner: MisagHostAssociated
    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
    multivalued: true
  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
    keywords:
    - sample
    - storage
    - temperature
    slot_uri: MIXS:0000110
    alias: samp_store_temp
    owner: MisagHostAssociated
    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
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_store_dur:
    name: samp_store_dur
    description: Duration for which the sample was stored. Indicate the duration for
      which the sample was stored written in ISO 8601 format
    title: sample storage duration
    examples:
    - value: P1Y6M
    from_schema: https://w3id.org/mixs
    keywords:
    - duration
    - period
    - sample
    - storage
    slot_uri: MIXS:0000116
    alias: samp_store_dur
    owner: MisagHostAssociated
    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
    pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
    structured_pattern:
      syntax: ^{duration}$
      interpolated: true
      partial_match: true
  samp_store_loc:
    name: samp_store_loc
    annotations:
      Expected_value:
        tag: Expected_value
        value: location name
    description: Location at which sample was stored, usually name of a specific freezer/room
    title: sample storage location
    examples:
    - value: Freezer no:5
    from_schema: https://w3id.org/mixs
    keywords:
    - location
    - sample
    - storage
    slot_uri: MIXS:0000755
    alias: samp_store_loc
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
  host_symbiont:
    name: host_symbiont
    annotations:
      Expected_value:
        tag: Expected_value
        value: species name or common name
    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
    keywords:
    - host
    - host.
    - observed
    - symbiosis
    slot_uri: MIXS:0001298
    alias: host_symbiont
    owner: MisagHostAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    multivalued: true
  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
    keywords:
    - parameter
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    alias: misc_param
    owner: MisagHostAssociated
    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
    multivalued: true
class_uri: MIXS:0010010_0016002