Combination: Mimag combined with PlantAssociated (MimagPlantAssociated)

MIxS Data that comply with the Mimag checklist and the PlantAssociated Extension

Composition

Mimag [Checklist] + PlantAssociated [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:0000080	mag_cov_software	0..1 MagCovSoftwareEnum	Tool(s) used to determine the genome coverage if coverage is used as a binnin...
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:0000077	bin_param	1 BinParamEnum	The parameters that have been applied during the extraction of genomes from m...
MIXS:0000078	bin_software	1 String	Tool(s) used for the extraction of genomes from metagenomic datasets, where p...
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:0000079	reassembly_bin	0..1 Boolean	Has an assembly been performed on a genome bin extracted from a metagenomic a...
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: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: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: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: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:0000551	air_temp_regm	* String	Information about treatment involving an exposure to varying temperatures; sh...
MIXS:0000247	ances_data	0..1 String	Information about either pedigree or other ancestral information description ...
MIXS:0000553	antibiotic_regm	* String	Information about treatment involving antibiotic administration; should inclu...
MIXS:0000858	biol_stat	0..1 BiolStatEnum	The level of genome modification
MIXS:0001038	biotic_regm	* String	Information about treatment(s) involving use of biotic factors, such as bacte...
MIXS:0000751	chem_administration	* String	List of chemical compounds administered to the host or site where sampling oc...
MIXS:0000555	chem_mutagen	* String	Treatment involving use of mutagens; should include the name of mutagen, amou...
MIXS:0001040	climate_environment	* String	Treatment involving an exposure to a particular climate; treatment regimen in...
MIXS:0001041	cult_root_med	0..1 String	Name or reference for the hydroponic or in vitro culture rooting medium; can ...
MIXS:0000556	fertilizer_regm	* String	Information about treatment involving the use of fertilizers; should include ...
MIXS:0000557	fungicide_regm	* String	Information about treatment involving use of fungicides; should include the n...
MIXS:0000558	gaseous_environment	* String	Use of conditions with differing gaseous environments; should include the nam...
MIXS:0000859	genetic_mod	0..1 String	Genetic modifications of the genome of an organism, which may occur naturally...
MIXS:0000559	gravity	* String	Information about treatment involving use of gravity factor to study various ...
MIXS:0001043	growth_facil	0..1 String	Type of facility where the sampled plant was grown; controlled vocabulary: gr...
MIXS:0001044	growth_habit	0..1 GrowthHabitEnum	Characteristic shape, appearance or growth form of a plant species
MIXS:0000560	growth_hormone_regm	* String	Information about treatment involving use of growth hormones; should include ...
MIXS:0000561	herbicide_regm	* String	Information about treatment involving use of herbicides; information about tr...
MIXS:0000255	host_age	0..1 String	Age of host at the time of sampling; relevant scale depends on species and st...
MIXS:0000248	host_common_name	0..1 String	Common name 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:0000257	host_dry_mass	0..1 String	Measurement of dry mass
MIXS:0000365	host_genotype	0..1 String	Observed genotype
MIXS:0000264	host_height	0..1 String	The height of subject
MIXS:0001318	host_subspecf_genlin	* String	Information about the genetic distinctness of the host organism below the sub...
MIXS:0000256	host_length	0..1 String	The length of subject
MIXS:0000251	host_life_stage	0..1 String	Description of life stage of host
MIXS:0000874	host_phenotype	0..1 String	Phenotype of human or other host
MIXS:0000250	host_taxid	0..1 String	NCBI taxon id of the host, e
MIXS:0000263	host_tot_mass	0..1 String	Total mass of the host at collection, the unit depends on host
MIXS:0000567	host_wet_mass	0..1 String	Measurement of wet mass
MIXS:0000568	humidity_regm	* String	Information about treatment involving an exposure to varying degree of humidi...
MIXS:0000569	light_regm	0..1 String	Information about treatment(s) involving exposure to light, including both li...
MIXS:0001052	mechanical_damage	* String	Information about any mechanical damage exerted on the plant; can include mul...
MIXS:0000570	mineral_nutr_regm	* String	Information about treatment involving the use of mineral supplements; should ...
MIXS:0000752	misc_param	* String	Any other measurement performed or parameter collected, that is not listed he...
MIXS:0000571	non_min_nutr_regm	* String	Information about treatment involving the exposure of plant to non-mineral nu...
MIXS:0000103	organism_count	* String	Total cell count of any organism (or group of organisms) per gram, volume or ...
MIXS:0000753	oxy_stat_samp	0..1 OxyStatSampEnum	Oxygenation status of sample
MIXS:0001056	ph_regm	* String	Information about treatment involving exposure of plants to varying levels of...
MIXS:0000754	perturbation	* String	Type of perturbation, e
MIXS:0000573	pesticide_regm	* String	Information about treatment involving use of insecticides; should include the...
MIXS:0001057	plant_growth_med	0..1 String	Specification of the media for growing the plants or tissue cultured samples,...
MIXS:0001058	plant_product	0..1 String	Substance produced by the plant, where the sample was obtained from
MIXS:0001059	plant_sex	0..1 PlantSexEnum	Sex of the reproductive parts on the whole plant, e
MIXS:0001060	plant_struc	0..1 String	Name of plant structure the sample was obtained from; for Plant Ontology (PO)...
MIXS:0000575	radiation_regm	* String	Information about treatment involving exposure of plant or a plant part to a ...
MIXS:0000576	rainfall_regm	* String	Information about treatment involving an exposure to a given amount of rainfa...
MIXS:0001061	root_cond	0..1 String	Relevant rooting conditions such as field plot size, sowing density, containe...
MIXS:0000577	root_med_carbon	0..1 String	Source of organic carbon in the culture rooting medium; e
MIXS:0000578	root_med_macronutr	0..1 String	Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);...
MIXS:0000579	root_med_micronutr	0..1 String	Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, ...
MIXS:0000580	root_med_suppl	0..1 String	Organic supplements of the culture rooting medium, such as vitamins, amino ac...
MIXS:0001062	root_med_ph	0..1 Float	pH measurement of the culture rooting medium; e
MIXS:0000581	root_med_regl	0..1 String	Growth regulators in the culture rooting medium such as cytokinins, auxins, g...
MIXS:0001063	root_med_solid	0..1 String	Specification of the solidifying agent in the culture rooting medium; e
MIXS:0000582	salt_regm	* String	Information about treatment involving use of salts as supplement to liquid an...
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:0000183	salinity	0..1 String	The total concentration of all dissolved salts in a liquid or solid sample
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:0000110	samp_store_temp	0..1 String	Temperature at which sample was stored, e
MIXS:0001068	season_environment	* String	Treatment involving an exposure to a particular season (e
MIXS:0001069	standing_water_regm	* String	Treatment involving an exposure to standing water during a plant's life span,...
MIXS:0001070	tiss_cult_growth_med	0..1 String	Description of plant tissue culture growth media used
MIXS:0000590	water_temp_regm	* String	Information about treatment involving an exposure to water with varying degre...
MIXS:0000591	watering_regm	* String	Information about treatment involving an exposure to watering frequencies, tr...
MIXS:0001298	host_symbiont	* String	The taxonomic name of the organism(s) found living in mutualistic, commensali...

LinkML Source

Direct

name: MimagPlantAssociated
description: MIxS Data that comply with the Mimag checklist and the PlantAssociated
  Extension
title: Mimag combined with PlantAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: PlantAssociated
mixins:
- Mimag
class_uri: MIXS:0010011_0016010

Induced

name: MimagPlantAssociated
description: MIxS Data that comply with the Mimag checklist and the PlantAssociated
  Extension
title: Mimag combined with PlantAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: PlantAssociated
mixins:
- Mimag
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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    domain_of:
    - Mimag
    - Misag
    - Miuvig
    range: string
  mag_cov_software:
    name: mag_cov_software
    description: Tool(s) used to determine the genome coverage if coverage is used
      as a binning parameter in the extraction of genomes from metagenomic datasets
    title: MAG coverage software
    examples:
    - value: bbmap
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    slot_uri: MIXS:0000080
    alias: mag_cov_software
    owner: MimagPlantAssociated
    domain_of:
    - Mimag
    - Miuvig
    range: MagCovSoftwareEnum
  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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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
  bin_param:
    name: bin_param
    description: The parameters that have been applied during the extraction of genomes
      from metagenomic datasets
    title: binning parameters
    examples:
    - value: coverage
      description: was 'coverage and kmer'
    - value: kmer
      description: was coverage and kmer
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - parameter
    slot_uri: MIXS:0000077
    alias: bin_param
    owner: MimagPlantAssociated
    domain_of:
    - Mimag
    - Miuvig
    range: BinParamEnum
    required: true
  bin_software:
    name: bin_software
    annotations:
      Expected_value:
        tag: Expected_value
        value: names and versions of software(s) used
    description: Tool(s) used for the extraction of genomes from metagenomic datasets,
      where possible include a product ID (PID) of the tool(s) used
    title: binning software
    examples:
    - value: MetaCluster-TA (RRID:SCR_004599), MaxBin (biotools:maxbin)
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    string_serialization: '{software};{version}{PID}'
    slot_uri: MIXS:0000078
    alias: bin_software
    owner: MimagPlantAssociated
    domain_of:
    - Mimag
    - Miuvig
    range: string
    required: 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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    domain_of:
    - MigsBa
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    range: RelToOxygenEnum
  reassembly_bin:
    name: reassembly_bin
    description: Has an assembly been performed on a genome bin extracted from a metagenomic
      assembly?
    title: reassembly post binning
    examples:
    - value: 'no'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - post
    slot_uri: MIXS:0000079
    alias: reassembly_bin
    owner: MimagPlantAssociated
    domain_of:
    - Mimag
    - Miuvig
    range: boolean
  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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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
  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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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
  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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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
  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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: string
    required: true
    pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
    structured_pattern:
      syntax: '^{text}: {text}, {text}$'
      interpolated: true
      partial_match: true
  collection_date:
    name: collection_date
    description: 'The time of sampling, either as an instance (single point in time)
      or interval. In case no exact time is available, the date/time can be right
      truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
      2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
    title: collection date
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - date
    slot_uri: MIXS:0000011
    alias: collection_date
    owner: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    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: MimagPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    multivalued: true
  air_temp_regm:
    name: air_temp_regm
    annotations:
      Expected_value:
        tag: Expected_value
        value: temperature value;treatment interval and duration
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: Information about treatment involving an exposure to varying temperatures;
      should include the temperature, treatment regimen including how many times the
      treatment was repeated, how long each treatment lasted, and the start and end
      time of the entire treatment; can include different temperature regimens
    title: air temperature regimen
    examples:
    - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - air
    - regimen
    - temperature
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000551
    alias: air_temp_regm
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    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: MimagPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    range: string
  antibiotic_regm:
    name: antibiotic_regm
    annotations:
      Expected_value:
        tag: Expected_value
        value: antibiotic name;antibiotic amount;treatment interval and duration
      Preferred_unit:
        tag: Preferred_unit
        value: milligram
    description: Information about treatment involving antibiotic administration;
      should include the name of antibiotic, amount administered, treatment regimen
      including how many times the treatment was repeated, how long each treatment
      lasted, and the start and end time of the entire treatment; can include multiple
      antibiotic regimens
    title: antibiotic regimen
    examples:
    - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - regimen
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000553
    alias: antibiotic_regm
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    multivalued: true
  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: MimagPlantAssociated
    domain_of:
    - HostAssociated
    - PlantAssociated
    range: BiolStatEnum
  biotic_regm:
    name: biotic_regm
    description: Information about treatment(s) involving use of biotic factors, such
      as bacteria, viruses or fungi
    title: biotic regimen
    examples:
    - value: sample inoculated with Rhizobium spp. Culture
    from_schema: https://w3id.org/mixs
    keywords:
    - regimen
    slot_uri: MIXS:0001038
    alias: biotic_regm
    owner: MimagPlantAssociated
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
    multivalued: true
  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: MimagPlantAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  chem_mutagen:
    name: chem_mutagen
    annotations:
      Expected_value:
        tag: Expected_value
        value: mutagen name;mutagen amount;treatment interval and duration
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter
    description: Treatment involving use of mutagens; should include the name of mutagen,
      amount administered, treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment; can include multiple mutagen regimens
    title: chemical mutagen
    examples:
    - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000555
    alias: chem_mutagen
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    multivalued: true
  climate_environment:
    name: climate_environment
    description: Treatment involving an exposure to a particular climate; treatment
      regimen including how many times the treatment was repeated, how long each treatment
      lasted, and the start and end time of the entire treatment; can include multiple
      climates
    title: climate environment
    examples:
    - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - environment
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001040
    alias: climate_environment
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    multivalued: true
  cult_root_med:
    name: cult_root_med
    annotations:
      Expected_value:
        tag: Expected_value
        value: name, PMID,DOI or url
    description: Name or reference for the hydroponic or in vitro culture rooting
      medium; can be the name of a commonly used medium or reference to a specific
      medium, e.g. Murashige and Skoog medium. If the medium has not been formally
      published, use the rooting medium descriptors
    title: culture rooting medium
    examples:
    - value: http://himedialabs.com/TD/PT158.pdf
    from_schema: https://w3id.org/mixs
    keywords:
    - culture
    string_serialization: '{text}|{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0001041
    alias: cult_root_med
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
  fertilizer_regm:
    name: fertilizer_regm
    annotations:
      Expected_value:
        tag: Expected_value
        value: fertilizer name;fertilizer amount;treatment interval and duration
      Preferred_unit:
        tag: Preferred_unit
        value: gram, mole per liter, milligram per liter
    description: Information about treatment involving the use of fertilizers; should
      include the name of fertilizer, amount administered, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple fertilizer
      regimens
    title: fertilizer regimen
    examples:
    - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - regimen
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000556
    alias: fertilizer_regm
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    multivalued: true
  fungicide_regm:
    name: fungicide_regm
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: gram, mole per liter, milligram per liter
    description: Information about treatment involving use of fungicides; should include
      the name of fungicide, amount administered, treatment regimen including how
      many times the treatment was repeated, how long each treatment lasted, and the
      start and end time of the entire treatment; can include multiple fungicide regimens
    title: fungicide regimen
    examples:
    - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - regimen
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000557
    alias: fungicide_regm
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    multivalued: true
  gaseous_environment:
    name: gaseous_environment
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter
    description: Use of conditions with differing gaseous environments; should include
      the name of gaseous compound, amount administered, treatment duration, interval
      and total experimental duration; can include multiple gaseous environment regimens
    title: gaseous environment
    examples:
    - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - environment
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000558
    alias: gaseous_environment
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    multivalued: true
  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: MimagPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - PlantAssociated
    range: string
  gravity:
    name: gravity
    annotations:
      Expected_value:
        tag: Expected_value
        value: gravity factor value;treatment interval and duration
      Preferred_unit:
        tag: Preferred_unit
        value: meter per square second, g
    description: Information about treatment involving use of gravity factor to study
      various types of responses in presence, absence or modified levels of gravity;
      treatment regimen including how many times the treatment was repeated, how long
      each treatment lasted, and the start and end time of the entire treatment; can
      include multiple treatments
    title: gravity
    examples:
    - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000559
    alias: gravity
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    multivalued: true
  growth_facil:
    name: growth_facil
    annotations:
      Expected_value:
        tag: Expected_value
        value: free text or CO
    description: 'Type of facility where the sampled plant was grown; controlled vocabulary:
      growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively
      use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'
    title: growth facility
    examples:
    - value: Growth chamber [CO_715:0000189]
    from_schema: https://w3id.org/mixs
    keywords:
    - facility
    - growth
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001043
    alias: growth_facil
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
  growth_habit:
    name: growth_habit
    description: Characteristic shape, appearance or growth form of a plant species
    title: growth habit
    examples:
    - value: spreading
    from_schema: https://w3id.org/mixs
    keywords:
    - growth
    slot_uri: MIXS:0001044
    alias: growth_habit
    owner: MimagPlantAssociated
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    range: GrowthHabitEnum
  growth_hormone_regm:
    name: growth_hormone_regm
    annotations:
      Expected_value:
        tag: Expected_value
        value: growth hormone name;growth hormone amount;treatment interval and duration
      Preferred_unit:
        tag: Preferred_unit
        value: gram, mole per liter, milligram per liter
    description: Information about treatment involving use of growth hormones; should
      include the name of growth hormone, amount administered, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple growth
      hormone regimens
    title: growth hormone regimen
    examples:
    - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - growth
    - regimen
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000560
    alias: growth_hormone_regm
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    multivalued: true
  herbicide_regm:
    name: herbicide_regm
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: gram, mole per liter, milligram per liter
    description: Information about treatment involving use of herbicides; information
      about treatment involving use of growth hormones; should include the name of
      herbicide, amount administered, treatment regimen including how many times the
      treatment was repeated, how long each treatment lasted, and the start and end
      time of the entire treatment; can include multiple regimens
    title: herbicide regimen
    examples:
    - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - regimen
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000561
    alias: herbicide_regm
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    multivalued: true
  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: MimagPlantAssociated
    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_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: rice
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000248
    alias: host_common_name
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    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: downy mildew
    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: MimagPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    range: string
  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: MimagPlantAssociated
    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_genotype:
    name: host_genotype
    description: Observed genotype
    title: host genotype
    examples:
    - value: Ts
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000365
    alias: host_genotype
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
  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: 1 meter
    from_schema: https://w3id.org/mixs
    keywords:
    - height
    - host
    - host.
    slot_uri: MIXS:0000264
    alias: host_height
    owner: MimagPlantAssociated
    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_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: MimagPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    range: string
    multivalued: 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: MimagPlantAssociated
    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_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: MimagPlantAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - 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: seed pod; green [PATO:0000320]
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000874
    alias: host_phenotype
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
  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: '4530'
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - taxon
    string_serialization: '{NCBI taxid}'
    slot_uri: MIXS:0000250
    alias: host_taxid
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - 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: MimagPlantAssociated
    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_wet_mass:
    name: host_wet_mass
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: kilogram, gram
    description: Measurement of wet mass
    title: host wet mass
    examples:
    - value: 1500 gram
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - mass
    - wet
    slot_uri: MIXS:0000567
    alias: host_wet_mass
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    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
  humidity_regm:
    name: humidity_regm
    annotations:
      Expected_value:
        tag: Expected_value
        value: humidity value;treatment interval and duration
      Preferred_unit:
        tag: Preferred_unit
        value: gram per cubic meter
    description: Information about treatment involving an exposure to varying degree
      of humidity; information about treatment involving use of growth hormones; should
      include amount of humidity administered, treatment regimen including how many
      times the treatment was repeated, how long each treatment lasted, and the start
      and end time of the entire treatment; can include multiple regimens
    title: humidity regimen
    examples:
    - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - humidity
    - regimen
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000568
    alias: humidity_regm
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    multivalued: true
  light_regm:
    name: light_regm
    annotations:
      Expected_value:
        tag: Expected_value
        value: exposure type;light intensity;light quality
      Preferred_unit:
        tag: Preferred_unit
        value: lux; micrometer, nanometer, angstrom
    description: Information about treatment(s) involving exposure to light, including
      both light intensity and quality
    title: light regimen
    examples:
    - value: incandescant light;10 lux;450 nanometer
    from_schema: https://w3id.org/mixs
    keywords:
    - light
    - regimen
    string_serialization: '{text};{float} {unit};{float} {unit}'
    slot_uri: MIXS:0000569
    alias: light_regm
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
  mechanical_damage:
    name: mechanical_damage
    annotations:
      Expected_value:
        tag: Expected_value
        value: damage type;body site
    description: Information about any mechanical damage exerted on the plant; can
      include multiple damages and sites
    title: mechanical damage
    examples:
    - value: pruning;bark
    from_schema: https://w3id.org/mixs
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0001052
    alias: mechanical_damage
    owner: MimagPlantAssociated
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
    multivalued: true
  mineral_nutr_regm:
    name: mineral_nutr_regm
    annotations:
      Expected_value:
        tag: Expected_value
        value: mineral nutrient name;mineral nutrient amount;treatment interval and
          duration
      Preferred_unit:
        tag: Preferred_unit
        value: gram, mole per liter, milligram per liter
    description: Information about treatment involving the use of mineral supplements;
      should include the name of mineral nutrient, amount administered, treatment
      regimen including how many times the treatment was repeated, how long each treatment
      lasted, and the start and end time of the entire treatment; can include multiple
      mineral nutrient regimens
    title: mineral nutrient regimen
    examples:
    - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - mineral
    - nutrient
    - regimen
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000570
    alias: mineral_nutr_regm
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    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: MimagPlantAssociated
    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
  non_min_nutr_regm:
    name: non_min_nutr_regm
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: gram, mole per liter, milligram per liter
    description: Information about treatment involving the exposure of plant to non-mineral
      nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral
      nutrient, amount administered, treatment regimen including how many times the
      treatment was repeated, how long each treatment lasted, and the start and end
      time of the entire treatment; can include multiple non-mineral nutrient regimens
    title: non-mineral nutrient regimen
    examples:
    - value: https://phylogenomics.me/protocols/16s-pcr-protocol/
    from_schema: https://w3id.org/mixs
    keywords:
    - non-mineral
    - nutrient
    - regimen
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000571
    alias: non_min_nutr_regm
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    multivalued: true
  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: MimagPlantAssociated
    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
  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: MimagPlantAssociated
    domain_of:
    - Agriculture
    - Air
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: OxyStatSampEnum
  ph_regm:
    name: ph_regm
    description: Information about treatment involving exposure of plants to varying
      levels of ph of the growth media, treatment regimen including how many times
      the treatment was repeated, how long each treatment lasted, and the start and
      end time of the entire treatment; can include multiple regimen
    title: pH regimen
    examples:
    - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - ph
    - regimen
    string_serialization: '{float};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001056
    alias: ph_regm
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    multivalued: true
  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: MimagPlantAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  pesticide_regm:
    name: pesticide_regm
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: gram, mole per liter, milligram per liter
    description: Information about treatment involving use of insecticides; should
      include the name of pesticide, amount administered, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple pesticide
      regimens
    title: pesticide regimen
    examples:
    - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - regimen
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000573
    alias: pesticide_regm
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    multivalued: true
  plant_growth_med:
    name: plant_growth_med
    annotations:
      Expected_value:
        tag: Expected_value
        value: EO or enumeration
    description: Specification of the media for growing the plants or tissue cultured
      samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in
      vitro liquid culture medium. Recommended value is a specific value from EO:plant
      growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147)
      or other controlled vocabulary
    title: plant growth medium
    examples:
    - value: hydroponic plant culture media [EO:0007067]
    from_schema: https://w3id.org/mixs
    keywords:
    - growth
    - plant
    string_serialization: '{termLabel} [{termID}] or [husk|other artificial liquid
      medium|other artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water]'
    slot_uri: MIXS:0001057
    alias: plant_growth_med
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
  plant_product:
    name: plant_product
    annotations:
      Expected_value:
        tag: Expected_value
        value: product name
    description: Substance produced by the plant, where the sample was obtained from
    title: plant product
    examples:
    - value: xylem sap [PO:0025539]
    from_schema: https://w3id.org/mixs
    keywords:
    - plant
    - product
    slot_uri: MIXS:0001058
    alias: plant_product
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
  plant_sex:
    name: plant_sex
    description: Sex of the reproductive parts on the whole plant, e.g. pistillate,
      staminate, monoecieous, hermaphrodite
    title: plant sex
    examples:
    - value: Hermaphroditic
    from_schema: https://w3id.org/mixs
    keywords:
    - plant
    slot_uri: MIXS:0001059
    alias: plant_sex
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: PlantSexEnum
  plant_struc:
    name: plant_struc
    description: Name of plant structure the sample was obtained from; for Plant Ontology
      (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,
      e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the
      sex of it can be recorded here
    title: plant structure
    examples:
    - value: epidermis [PO:0005679]
    from_schema: https://w3id.org/mixs
    keywords:
    - plant
    slot_uri: MIXS:0001060
    alias: plant_struc
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    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
  radiation_regm:
    name: radiation_regm
    annotations:
      Expected_value:
        tag: Expected_value
        value: radiation type name;radiation amount;treatment interval and duration
      Preferred_unit:
        tag: Preferred_unit
        value: rad, gray
    description: Information about treatment involving exposure of plant or a plant
      part to a particular radiation regimen; should include the radiation type, amount
      or intensity administered, treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment; can include multiple radiation regimens
    title: radiation regimen
    examples:
    - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - regimen
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000575
    alias: radiation_regm
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    multivalued: true
  rainfall_regm:
    name: rainfall_regm
    annotations:
      Expected_value:
        tag: Expected_value
        value: measurement value;treatment interval and duration
      Preferred_unit:
        tag: Preferred_unit
        value: millimeter
    description: Information about treatment involving an exposure to a given amount
      of rainfall, treatment regimen including how many times the treatment was repeated,
      how long each treatment lasted, and the start and end time of the entire treatment;
      can include multiple regimens
    title: rainfall regimen
    examples:
    - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - rain
    - regimen
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000576
    alias: rainfall_regm
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    multivalued: true
  root_cond:
    name: root_cond
    description: Relevant rooting conditions such as field plot size, sowing density,
      container dimensions, number of plants per container
    title: rooting conditions
    examples:
    - value: http://himedialabs.com/TD/PT158.pdf
    from_schema: https://w3id.org/mixs
    keywords:
    - condition
    slot_uri: MIXS:0001061
    alias: root_cond
    owner: MimagPlantAssociated
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    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
  root_med_carbon:
    name: root_med_carbon
    annotations:
      Expected_value:
        tag: Expected_value
        value: carbon source name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter
    description: Source of organic carbon in the culture rooting medium; e.g. sucrose
    title: rooting medium carbon
    examples:
    - value: sucrose
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000577
    alias: root_med_carbon
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
  root_med_macronutr:
    name: root_med_macronutr
    annotations:
      Expected_value:
        tag: Expected_value
        value: macronutrient name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter
    description: Measurement of the culture rooting medium macronutrients (N,P, K,
      Ca, Mg, S); e.g. KH2PO4 (170 mg/L)
    title: rooting medium macronutrients
    examples:
    - value: KH2PO4;170  milligram per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - macronutrients
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000578
    alias: root_med_macronutr
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
  root_med_micronutr:
    name: root_med_micronutr
    annotations:
      Expected_value:
        tag: Expected_value
        value: micronutrient name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter
    description: Measurement of the culture rooting medium micronutrients (Fe, Mn,
      Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L)
    title: rooting medium micronutrients
    examples:
    - value: H3BO3;6.2  milligram per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - micronutrients
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000579
    alias: root_med_micronutr
    owner: MimagPlantAssociated
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
  root_med_suppl:
    name: root_med_suppl
    annotations:
      Expected_value:
        tag: Expected_value
        value: supplement name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter
    description: Organic supplements of the culture rooting medium, such as vitamins,
      amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid
      (0.5  mg/L)
    title: rooting medium organic supplements
    examples:
    - value: nicotinic acid;0.5 milligram per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - organic
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000580
    alias: root_med_suppl
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
  root_med_ph:
    name: root_med_ph
    description: pH measurement of the culture rooting medium; e.g. 5.5
    title: rooting medium pH
    examples:
    - value: '7.5'
    from_schema: https://w3id.org/mixs
    keywords:
    - ph
    slot_uri: MIXS:0001062
    alias: root_med_ph
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - PlantAssociated
    range: float
  root_med_regl:
    name: root_med_regl
    annotations:
      Expected_value:
        tag: Expected_value
        value: regulator name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter
    description: Growth regulators in the culture rooting medium such as cytokinins,
      auxins, gybberellins, abscisic acid; e.g. 0.5  mg/L NAA
    title: rooting medium regulators
    examples:
    - value: abscisic acid;0.75 milligram per liter
    from_schema: https://w3id.org/mixs
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000581
    alias: root_med_regl
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
  root_med_solid:
    name: root_med_solid
    description: Specification of the solidifying agent in the culture rooting medium;
      e.g. agar
    title: rooting medium solidifier
    examples:
    - value: agar
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0001063
    alias: root_med_solid
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
  salt_regm:
    name: salt_regm
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: gram, microgram, mole per liter, gram per liter
    description: Information about treatment involving use of salts as supplement
      to liquid and soil growth media; should include the name of salt, amount administered,
      treatment regimen including how many times the treatment was repeated, how long
      each treatment lasted, and the start and end time of the entire treatment; can
      include multiple salt regimens
    title: salt regimen
    examples:
    - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - regimen
    - salt
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000582
    alias: salt_regm
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    multivalued: true
  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: MimagPlantAssociated
    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: MimagPlantAssociated
    domain_of:
    - HostAssociated
    - PlantAssociated
    range: SampDisStageEnum
  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: MimagPlantAssociated
    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
  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: MimagPlantAssociated
    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: MimagPlantAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
  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: MimagPlantAssociated
    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
  season_environment:
    name: season_environment
    description: Treatment involving an exposure to a particular season (e.g. Winter,
      summer, rabi, rainy etc.), treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment
    title: seasonal environment
    examples:
    - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - environment
    - season
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001068
    alias: season_environment
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    multivalued: true
  standing_water_regm:
    name: standing_water_regm
    description: Treatment involving an exposure to standing water during a plant's
      life span, types can be flood water or standing water, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple regimens
    title: standing water regimen
    examples:
    - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - regimen
    - water
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001069
    alias: standing_water_regm
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    multivalued: true
  tiss_cult_growth_med:
    name: tiss_cult_growth_med
    description: Description of plant tissue culture growth media used
    title: tissue culture growth media
    examples:
    - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf
    from_schema: https://w3id.org/mixs
    keywords:
    - culture
    - growth
    slot_uri: MIXS:0001070
    alias: tiss_cult_growth_med
    owner: MimagPlantAssociated
    domain_of:
    - PlantAssociated
    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
  water_temp_regm:
    name: water_temp_regm
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Information about treatment involving an exposure to water with varying
      degree of temperature, treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment; can include multiple regimens
    title: water temperature regimen
    examples:
    - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - regimen
    - temperature
    - water
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000590
    alias: water_temp_regm
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    multivalued: true
  watering_regm:
    name: watering_regm
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milliliter, liter
    description: Information about treatment involving an exposure to watering frequencies,
      treatment regimen including how many times the treatment was repeated, how long
      each treatment lasted, and the start and end time of the entire treatment; can
      include multiple regimens
    title: watering regimen
    examples:
    - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - regimen
    - water
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000591
    alias: watering_regm
    owner: MimagPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    multivalued: true
  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: MimagPlantAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    multivalued: true
class_uri: MIXS:0010011_0016010