Class: MimarksSPlantAssociated

MIxS data that complies with the MimarksS checklist and the PlantAssociated environmental package

URI: MIXS:0010008_0016010

Inheritance

• EnvironmentalPackage
  • PlantAssociated
    • MimarksSPlantAssociated [ MimarksS]

Slots

Name	Cardinality and Range	Description	Inheritance
mid	0..1 recommended String	Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe...	MimarksS
samp_name	1..1 String	A local identifier or name that for the material sample used for extracting n...	PlantAssociated, MimarksS
alt	0..1 recommended String	Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba...	MimarksS
neg_cont_type	0..1 recommended NEGCONTTYPEENUM	The substance or equipment used as a negative control in an investigation	MimarksS
samp_mat_process	0..1 recommended String	A brief description of any processing applied to the sample during or after r...	MimarksS
elev	0..1 recommended String	Elevation of the sampling site is its height above a fixed reference point, m...	PlantAssociated, MimarksS
source_mat_id	0..* recommended String	A unique identifier assigned to a material sample (as defined by http://rs	MimarksS
lib_size	0..1 recommended Integer	Total number of clones in the library prepared for the project	MimarksS
samp_collect_device	0..1 recommended String	The device used to collect an environmental sample	MimarksS
rel_to_oxygen	0..1 RELTOOXYGENENUM	Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ...	MimarksS
size_frac	0..1 String	Filtering pore size used in sample preparation	MimarksS
adapters	0..1 recommended String	Adapters provide priming sequences for both amplification and sequencing of t...	MimarksS
assembly_software	0..1 recommended String	Tool(s) used for assembly, including version number and parameters	MimarksS
samp_collect_method	0..1 recommended String	The method employed for collecting the sample	MimarksS
seq_quality_check	0..1 recommended SEQQUALITYCHECKENUM	Indicate if the sequence has been called by automatic systems (none) or under...	MimarksS
collection_date	1..1 Datetime	The time of sampling, either as an instance (single point in time) or interva...	MimarksS
pcr_primers	0..1 recommended String	PCR primers that were used to amplify the sequence of the targeted gene, locu...	MimarksS
geo_loc_name	1..1 String	The geographical origin of the sample as defined by the country or sea name f...	MimarksS
nucl_acid_amp	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...	MimarksS
samp_taxon_id	1..1 String	NCBI taxon id of the sample	MimarksS
lib_layout	0..1 recommended LIBLAYOUTENUM	Specify whether to expect single, paired, or other configuration of reads	MimarksS
env_medium	1..1 String	Report the environmental material(s) immediately surrounding the sample or sp...	MimarksS
target_subfragment	0..1 recommended String	Name of subfragment of a gene or locus	MimarksS
samp_size	0..1 recommended String	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...	MimarksS
lib_reads_seqd	0..1 recommended Integer	Total number of clones sequenced from the library	MimarksS
seq_meth	1..1 String	Sequencing machine used	MimarksS
temp	0..1 recommended String	Temperature of the sample at the time of sampling	PlantAssociated, MimarksS
experimental_factor	0..* recommended String	Variable aspects of an experiment design that can be used to describe an expe...	MimarksS
lib_vector	0..1 recommended String	Cloning vector type(s) used in construction of libraries	MimarksS
pcr_cond	0..1 recommended String	Description of reaction conditions and components of PCR in the form of 'init...	MimarksS
samp_vol_we_dna_ext	0..1 String	Volume (ml) or mass (g) of total collected sample processed for DNA extractio...	PlantAssociated, MimarksS
pos_cont_type	0..1 recommended String	The substance, mixture, product, or apparatus used to verify that a process w...	MimarksS
env_local_scale	1..1 String	Report the entity or entities which are in the sample or specimen s local vic...	MimarksS
env_broad_scale	1..1 String	Report the major environmental system the sample or specimen came from	MimarksS
nucl_acid_ext	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...	MimarksS
chimera_check	0..1 recommended String	Tool(s) used for chimera checking, including version number and parameters, t...	MimarksS
lat_lon	1..1 String	The geographical origin of the sample as defined by latitude and longitude	MimarksS
depth	0..1 recommended String	The vertical distance below local surface	PlantAssociated, MimarksS
project_name	1..1 String	Name of the project within which the sequencing was organized	PlantAssociated, MimarksS
target_gene	1..1 String	Targeted gene or locus name for marker gene studies	MimarksS
lib_screen	0..1 recommended String	Specific enrichment or screening methods applied before and/or after creating...	MimarksS
associated_resource	0..* recommended String	A related resource that is referenced, cited, or otherwise associated to the ...	MimarksS
sop	0..* recommended String	Standard operating procedures used in assembly and/or annotation of genomes, ...	MimarksS
air_temp_regm	0..* String	Information about treatment involving an exposure to varying temperatures; sh...	PlantAssociated
ances_data	0..1 String	Information about either pedigree or other ancestral information description ...	PlantAssociated
antibiotic_regm	0..* String	Information about treatment involving antibiotic administration; should inclu...	PlantAssociated
biol_stat	0..1 String	The level of genome modification	PlantAssociated
biotic_regm	0..* String	Information about treatment(s) involving use of biotic factors, such as bacte...	PlantAssociated
chem_administration	0..* String	List of chemical compounds administered to the host or site where sampling oc...	PlantAssociated
chem_mutagen	0..* String	Treatment involving use of mutagens; should include the name of mutagen, amou...	PlantAssociated
climate_environment	0..* String	Treatment involving an exposure to a particular climate; treatment regimen in...	PlantAssociated
cult_root_med	0..1 String	Name or reference for the hydroponic or in vitro culture rooting medium; can ...	PlantAssociated
fertilizer_regm	0..* String	Information about treatment involving the use of fertilizers; should include ...	PlantAssociated
fungicide_regm	0..* String	Information about treatment involving use of fungicides; should include the n...	PlantAssociated
gaseous_environment	0..* String	Use of conditions with differing gaseous environments; should include the nam...	PlantAssociated
genetic_mod	0..1 String	Genetic modifications of the genome of an organism, which may occur naturally...	PlantAssociated
gravity	0..* String	Information about treatment involving use of gravity factor to study various ...	PlantAssociated
growth_facil	0..1 String	Type of facility where the sampled plant was grown; controlled vocabulary: gr...	PlantAssociated
growth_habit	0..1 GROWTHHABITENUM	Characteristic shape, appearance or growth form of a plant species	PlantAssociated
growth_hormone_regm	0..* String	Information about treatment involving use of growth hormones; should include ...	PlantAssociated
herbicide_regm	0..* String	Information about treatment involving use of herbicides; information about tr...	PlantAssociated
host_age	0..1 String	Age of host at the time of sampling; relevant scale depends on species and st...	PlantAssociated
host_common_name	0..1 String	Common name of the host	PlantAssociated
host_disease_stat	0..1 String	List of diseases with which the host has been diagnosed; can include multiple...	PlantAssociated
host_dry_mass	0..1 String	Measurement of dry mass	PlantAssociated
host_genotype	0..1 String	Observed genotype	PlantAssociated
host_height	0..1 String	The height of subject	PlantAssociated
host_subspecf_genlin	0..* String	Information about the genetic distinctness of the host organism below the sub...	PlantAssociated
host_length	0..1 String	The length of subject	PlantAssociated
host_life_stage	0..1 String	Description of life stage of host	PlantAssociated
host_phenotype	0..1 String	Phenotype of human or other host	PlantAssociated
host_taxid	0..1 String	NCBI taxon id of the host, e	PlantAssociated
host_tot_mass	0..1 String	Total mass of the host at collection, the unit depends on host	PlantAssociated
host_wet_mass	0..1 String	Measurement of wet mass	PlantAssociated
humidity_regm	0..* String	Information about treatment involving an exposure to varying degree of humidi...	PlantAssociated
light_regm	0..1 String	Information about treatment(s) involving exposure to light, including both li...	PlantAssociated
mechanical_damage	0..* String	Information about any mechanical damage exerted on the plant; can include mul...	PlantAssociated
mineral_nutr_regm	0..* String	Information about treatment involving the use of mineral supplements; should ...	PlantAssociated
misc_param	0..* String	Any other measurement performed or parameter collected, that is not listed he...	PlantAssociated
non_min_nutr_regm	0..* String	Information about treatment involving the exposure of plant to non-mineral nu...	PlantAssociated
organism_count	0..* String	Total cell count of any organism (or group of organisms) per gram, volume or ...	PlantAssociated
oxy_stat_samp	0..1 OXYSTATSAMPENUM	Oxygenation status of sample	PlantAssociated
ph_regm	0..* String	Information about treatment involving exposure of plants to varying levels of...	PlantAssociated
perturbation	0..* String	Type of perturbation, e	PlantAssociated
pesticide_regm	0..* String	Information about treatment involving use of insecticides; should include the...	PlantAssociated
plant_growth_med	0..1 String	Specification of the media for growing the plants or tissue cultured samples,...	PlantAssociated
plant_product	0..1 String	Substance produced by the plant, where the sample was obtained from	PlantAssociated
plant_sex	0..1 PLANTSEXENUM	Sex of the reproductive parts on the whole plant, e	PlantAssociated
plant_struc	0..1 String	Name of plant structure the sample was obtained from; for Plant Ontology (PO)...	PlantAssociated
radiation_regm	0..* String	Information about treatment involving exposure of plant or a plant part to a ...	PlantAssociated
rainfall_regm	0..* String	Information about treatment involving an exposure to a given amount of rainfa...	PlantAssociated
root_cond	0..1 String	Relevant rooting conditions such as field plot size, sowing density, containe...	PlantAssociated
root_med_carbon	0..1 String	Source of organic carbon in the culture rooting medium; e	PlantAssociated
root_med_macronutr	0..1 String	Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);...	PlantAssociated
root_med_micronutr	0..1 String	Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, ...	PlantAssociated
root_med_suppl	0..1 String	Organic supplements of the culture rooting medium, such as vitamins, amino ac...	PlantAssociated
root_med_ph	0..1 Float	pH measurement of the culture rooting medium; e	PlantAssociated
root_med_regl	0..1 String	Growth regulators in the culture rooting medium such as cytokinins, auxins, g...	PlantAssociated
root_med_solid	0..1 String	Specification of the solidifying agent in the culture rooting medium; e	PlantAssociated
salt_regm	0..* String	Information about treatment involving use of salts as supplement to liquid an...	PlantAssociated
samp_capt_status	0..1 SAMPCAPTSTATUSENUM	Reason for the sample	PlantAssociated
samp_dis_stage	0..1 SAMPDISSTAGEENUM	Stage of the disease at the time of sample collection, e	PlantAssociated
salinity	0..1 String	The total concentration of all dissolved salts in a liquid or solid sample	PlantAssociated
samp_store_dur	0..1 String	Duration for which the sample was stored	PlantAssociated
samp_store_loc	0..1 String	Location at which sample was stored, usually name of a specific freezer/room	PlantAssociated
samp_store_temp	0..1 String	Temperature at which sample was stored, e	PlantAssociated
season_environment	0..* String	Treatment involving an exposure to a particular season (e	PlantAssociated
standing_water_regm	0..* String	Treatment involving an exposure to standing water during a plant's life span,...	PlantAssociated
tiss_cult_growth_med	0..1 String	Description of plant tissue culture growth media used	PlantAssociated
water_temp_regm	0..* String	Information about treatment involving an exposure to water with varying degre...	PlantAssociated
watering_regm	0..* String	Information about treatment involving an exposure to watering frequencies, tr...	PlantAssociated
host_symbiont	0..* String	The taxonomic name of the organism(s) found living in mutualistic, commensali...	PlantAssociated

Usages

used by	used in	type	used
MixsCompliantData	mimarks_s_plant_associated_data	range	MimarksSPlantAssociated

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc

Mappings

Mapping Type	Mapped Value
self	MIXS:0010008_0016010
native	mixs_6_2_rc:MimarksSPlantAssociated

LinkML Source

Direct

name: MimarksSPlantAssociated
description: MIxS data that complies with the MimarksS checklist and the PlantAssociated
  environmental package
title: MimarksS combined with PlantAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
is_a: PlantAssociated
mixins:
- MimarksS
class_uri: MIXS:0010008_0016010

Induced

name: MimarksSPlantAssociated
description: MIxS data that complies with the MimarksS checklist and the PlantAssociated
  environmental package
title: MimarksS combined with PlantAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
is_a: PlantAssociated
mixins:
- MimarksS
attributes:
  mid:
    name: mid
    description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
      used to specifically tag unique samples in a sequencing run. Sequence should
      be reported in uppercase letters
    title: multiplex identifiers
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000047
    multivalued: false
    alias: mid
    owner: MimarksSPlantAssociated
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^[ACGTRKSYMWBHDVN]+$
    structured_pattern:
      syntax: ^{ambiguous_nucleotides}$
      interpolated: true
      partial_match: true
  samp_name:
    name: samp_name
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ''
    description: A local identifier or name that for the material sample used for
      extracting nucleic acids, and subsequent sequencing. It can refer either to
      the original material collected or to any derived sub-samples. It can have any
      format, but we suggest that you make it concise, unique and consistent within
      your lab, and as informative as possible. INSDC requires every sample name from
      a single Submitter to be unique. Use of a globally unique identifier for the
      field source_mat_id is recommended in addition to sample_name
    title: sample name
    examples:
    - value: ISDsoil1
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001107
    multivalued: false
    alias: samp_name
    owner: MimarksSPlantAssociated
    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
  alt:
    name: alt
    description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric
      balloons and heights of places such as atmospheric layers and clouds. It is
      used to measure the height of an object which is above the earth's surface.
      In this context, the altitude measurement is the vertical distance between the
      earth's surface above sea level and the sampled position in the air
    title: altitude
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000094
    multivalued: false
    alias: alt
    owner: MimarksSPlantAssociated
    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
  neg_cont_type:
    name: neg_cont_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration or text
    description: The substance or equipment used as a negative control in an investigation
    title: negative control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001321
    multivalued: false
    alias: neg_cont_type
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: NEG_CONT_TYPE_ENUM
    recommended: true
  samp_mat_process:
    name: samp_mat_process
    description: A brief description of any processing applied to the sample during
      or after retrieving the sample from environment, or a link to the relevant protocol(s)
      performed
    title: sample material processing
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000016
    multivalued: false
    alias: samp_mat_process
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  elev:
    name: elev
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit
    title: elevation
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000093
    multivalued: false
    alias: elev
    owner: MimarksSPlantAssociated
    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
  source_mat_id:
    name: source_mat_id
    description: A unique identifier assigned to a material sample (as defined by
      http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
      digital record of a material sample) used for extracting nucleic acids, and
      subsequent sequencing. The identifier can refer either to the original material
      collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
      /bio_material, or /culture_collection may or may not share the same value as
      the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
      may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
      sampled tissue with the same identifier. However, the /culture_collection qualifier
      may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
      would refer to an identifier from some derived culture from which the nucleic
      acids were extracted (e.g. xatc123 or ark:/2154/R2)
    title: source material identifiers
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000026
    multivalued: true
    alias: source_mat_id
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - SymbiontAssociated
    range: string
    recommended: true
  lib_size:
    name: lib_size
    description: Total number of clones in the library prepared for the project
    title: library size
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000039
    multivalued: false
    alias: lib_size
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    recommended: true
  samp_collect_device:
    name: samp_collect_device
    description: The device used to collect an environmental sample. This field accepts
      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
    title: sample collection device
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000002
    multivalued: false
    alias: samp_collect_device
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
  rel_to_oxygen:
    name: rel_to_oxygen
    description: Is this organism an aerobe, anaerobe? Please note that aerobic and
      anaerobic are valid descriptors for microbial environments
    title: relationship to oxygen
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000015
    multivalued: false
    alias: rel_to_oxygen
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    range: REL_TO_OXYGEN_ENUM
    required: false
    recommended: false
  size_frac:
    name: size_frac
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    multivalued: false
    alias: size_frac
    owner: MimarksSPlantAssociated
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  adapters:
    name: adapters
    description: Adapters provide priming sequences for both amplification and sequencing
      of the sample-library fragments. Both adapters should be reported; in uppercase
      letters
    title: adapters
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{dna};{dna}'
    slot_uri: MIXS:0000048
    multivalued: false
    alias: adapters
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  assembly_software:
    name: assembly_software
    description: Tool(s) used for assembly, including version number and parameters
    title: assembly software
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000058
    multivalued: false
    alias: assembly_software
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: 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
  samp_collect_method:
    name: samp_collect_method
    description: The method employed for collecting the sample
    title: sample collection method
    examples:
    - value: swabbing
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001225
    multivalued: false
    alias: samp_collect_method
    owner: MimarksSPlantAssociated
    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
  seq_quality_check:
    name: seq_quality_check
    description: Indicate if the sequence has been called by automatic systems (none)
      or undergone a manual editing procedure (e.g. by inspecting the raw data or
      chromatograms). Applied only for sequences that are not submitted to SRA,ENA
      or DRA
    title: sequence quality check
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000051
    multivalued: false
    alias: seq_quality_check
    owner: MimarksSPlantAssociated
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: SEQ_QUALITY_CHECK_ENUM
    recommended: true
  collection_date:
    name: collection_date
    description: 'The time of sampling, either as an instance (single point in time)
      or interval. In case no exact time is available, the date/time can be right
      truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
      2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
    title: collection date
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000011
    multivalued: false
    alias: collection_date
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: datetime
    required: true
  pcr_primers:
    name: pcr_primers
    description: PCR primers that were used to amplify the sequence of the targeted
      gene, locus or subfragment. This field should contain all the primers used for
      a single PCR reaction if multiple forward or reverse primers are present in
      a single PCR reaction. The primer sequence should be reported in uppercase letters
    title: pcr primers
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: FWD:{dna};REV:{dna}
    slot_uri: MIXS:0000046
    multivalued: false
    alias: pcr_primers
    owner: MimarksSPlantAssociated
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  geo_loc_name:
    name: geo_loc_name
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name. Country or sea names should be chosen
      from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
      (http://purl.bioontology.org/ontology/GAZ)
    title: geographic location (country and/or sea,region)
    examples:
    - value: 'USA: Maryland, Bethesda'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000010
    multivalued: false
    alias: geo_loc_name
    owner: MimarksSPlantAssociated
    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
  nucl_acid_amp:
    name: nucl_acid_amp
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the enzymatic amplification (PCR,
      TMA, NASBA) of specific nucleic acids
    title: nucleic acid amplification
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000038
    multivalued: false
    alias: nucl_acid_amp
    owner: MimarksSPlantAssociated
    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
  samp_taxon_id:
    name: samp_taxon_id
    description: NCBI taxon id of the sample.  Maybe be a single taxon or mixed taxa
      sample. Use 'synthetic metagenome  for mock community/positive controls, or
      'blank sample' for negative controls
    title: taxonomy ID of DNA sample
    examples:
    - value: Gut Metagenome [NCBITaxon:749906]
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001320
    multivalued: false
    alias: samp_taxon_id
    owner: MimarksSPlantAssociated
    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
  lib_layout:
    name: lib_layout
    description: Specify whether to expect single, paired, or other configuration
      of reads
    title: library layout
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000041
    multivalued: false
    alias: lib_layout
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: LIB_LAYOUT_ENUM
    recommended: true
  env_medium:
    name: env_medium
    description: 'Report the environmental material(s) immediately surrounding the
      sample or specimen at the time of sampling. We recommend using subclasses of
      ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
      documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
      . Terms from other OBO ontologies are permissible as long as they reference
      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
      (e.g. a tree, a leaf, a table top)'
    title: environmental medium
    examples:
    - value: bluegrass field soil [ENVO:00005789]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000014
    multivalued: false
    alias: env_medium
    owner: MimarksSPlantAssociated
    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
  target_subfragment:
    name: target_subfragment
    description: Name of subfragment of a gene or locus. Important to e.g. identify
      special regions on marker genes like V6 on 16S rRNA
    title: target subfragment
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000045
    multivalued: false
    alias: target_subfragment
    owner: MimarksSPlantAssociated
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  samp_size:
    name: samp_size
    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
      sample collected
    title: amount or size of sample collected
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000001
    multivalued: false
    alias: samp_size
    owner: MimarksSPlantAssociated
    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
  lib_reads_seqd:
    name: lib_reads_seqd
    description: Total number of clones sequenced from the library
    title: library reads sequenced
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000040
    multivalued: false
    alias: lib_reads_seqd
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    recommended: true
  seq_meth:
    name: seq_meth
    description: Sequencing machine used. Where possible the term should be taken
      from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)
    title: sequencing method
    examples:
    - value: 454 Genome Sequencer FLX [OBI:0000702]
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000050
    multivalued: false
    alias: seq_meth
    owner: MimarksSPlantAssociated
    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
  temp:
    name: temp
    description: Temperature of the sample at the time of sampling
    title: temperature
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000113
    multivalued: false
    alias: temp
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  experimental_factor:
    name: experimental_factor
    description: Variable aspects of an experiment design that can be used to describe
      an experiment, or set of experiments, in an increasingly detailed manner. This
      field accepts ontology terms from Experimental Factor Ontology (EFO) and/or
      Ontology for Biomedical Investigations (OBI)
    title: experimental factor
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000008
    multivalued: true
    alias: experimental_factor
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  lib_vector:
    name: lib_vector
    description: Cloning vector type(s) used in construction of libraries
    title: library vector
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000042
    multivalued: false
    alias: lib_vector
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  pcr_cond:
    name: pcr_cond
    description: Description of reaction conditions and components of PCR in the form
      of 'initial denaturation:94degC_1.5min; annealing=...'
    title: pcr conditions
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
      elongation:degrees_minutes;total cycles
    slot_uri: MIXS:0000049
    multivalued: false
    alias: pcr_cond
    owner: MimarksSPlantAssociated
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  samp_vol_we_dna_ext:
    name: samp_vol_we_dna_ext
    description: 'Volume (ml) or mass (g) of total collected sample processed for
      DNA extraction. Note: total sample collected should be entered under the term
      Sample Size (MIXS:0000001)'
    title: sample volume or weight for DNA extraction
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000111
    multivalued: false
    alias: samp_vol_we_dna_ext
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  pos_cont_type:
    name: pos_cont_type
    description: The substance, mixture, product, or apparatus used to verify that
      a process which is part of an investigation delivers a true positive
    title: positive control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    multivalued: false
    alias: pos_cont_type
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    recommended: true
  env_local_scale:
    name: env_local_scale
    annotations:
      Expected_value:
        tag: Expected_value
        value: Environmental entities having causal influences upon the entity at
          time of sampling
    description: 'Report the entity or entities which are in the sample or specimen
      s local vicinity and which you believe have significant causal influences on
      your sample or specimen. We recommend using EnvO terms which are of smaller
      spatial grain than your entry for env_broad_scale. Terms, such as anatomical
      sites, from other OBO Library ontologies which interoperate with EnvO (e.g.
      UBERON) are accepted in this field. EnvO documentation about how to use the
      field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: local environmental context
    examples:
    - value: hillside [ENVO:01000333]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000013
    multivalued: false
    alias: env_local_scale
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: 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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000012
    multivalued: false
    alias: env_broad_scale
    owner: MimarksSPlantAssociated
    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
  nucl_acid_ext:
    name: nucl_acid_ext
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the material separation to recover
      the nucleic acid fraction from a sample
    title: nucleic acid extraction
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000037
    multivalued: false
    alias: nucl_acid_ext
    owner: MimarksSPlantAssociated
    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
  chimera_check:
    name: chimera_check
    description: Tool(s) used for chimera checking, including version number and parameters,
      to discover and remove chimeric sequences. A chimeric sequence is comprised
      of two or more phylogenetically distinct parent sequences
    title: chimera check software
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000052
    multivalued: false
    alias: chimera_check
    owner: MimarksSPlantAssociated
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: 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
  lat_lon:
    name: lat_lon
    annotations:
      Expected_value:
        tag: Expected_value
        value: decimal degrees,  limit to 8 decimal points
    description: The geographical origin of the sample as defined by latitude and
      longitude. The values should be reported in decimal degrees and in WGS84 system
    title: geographic location (latitude and longitude)
    examples:
    - value: 50.586825 6.408977
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{float} {float}'
    slot_uri: MIXS:0000009
    alias: lat_lon
    owner: MimarksSPlantAssociated
    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
  depth:
    name: depth
    description: The vertical distance below local surface. For sediment or soil samples
      depth is measured from sediment or soil surface, respectively. Depth can be
      reported as an interval for subsurface samples
    title: depth
    examples:
    - value: 10 meter
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000018
    multivalued: false
    alias: depth
    owner: MimarksSPlantAssociated
    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
  project_name:
    name: project_name
    description: Name of the project within which the sequencing was organized
    title: project name
    examples:
    - value: Forest soil metagenome
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000092
    multivalued: false
    alias: project_name
    owner: MimarksSPlantAssociated
    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
  target_gene:
    name: target_gene
    description: Targeted gene or locus name for marker gene studies
    title: target gene
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000044
    multivalued: false
    alias: target_gene
    owner: MimarksSPlantAssociated
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    required: true
  lib_screen:
    name: lib_screen
    description: Specific enrichment or screening methods applied before and/or after
      creating libraries
    title: library screening strategy
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000043
    multivalued: false
    alias: lib_screen
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  associated_resource:
    name: associated_resource
    annotations:
      Expected_value:
        tag: Expected_value
        value: reference to resource
    description: A related resource that is referenced, cited, or otherwise associated
      to the sequence
    title: relevant electronic resources
    examples:
    - value: http://www.earthmicrobiome.org/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000091
    multivalued: true
    alias: associated_resource
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  sop:
    name: sop
    description: Standard operating procedures used in assembly and/or annotation
      of genomes, metagenomes or environmental sequences
    title: relevant standard operating procedures
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000090
    multivalued: true
    alias: sop
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: 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-6-2-rc/mixs_6_2_rc
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000551
    multivalued: true
    alias: air_temp_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000247
    multivalued: false
    alias: ances_data
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000553
    multivalued: true
    alias: antibiotic_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  biol_stat:
    name: biol_stat
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration
    description: The level of genome modification
    title: biological status
    examples:
    - value: natural
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '[wild|natural|semi-natural|inbred line|breeder''s line|hybrid|clonal
      selection|mutant]'
    slot_uri: MIXS:0000858
    multivalued: false
    alias: biol_stat
    owner: MimarksSPlantAssociated
    domain_of:
    - HostAssociated
    - PlantAssociated
    range: string
    required: false
    recommended: false
  biotic_regm:
    name: biotic_regm
    description: Information about treatment(s) involving use of biotic factors, such
      as bacteria, viruses or fungi
    title: biotic regimen
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001038
    multivalued: true
    alias: biotic_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
    required: false
    recommended: false
  chem_administration:
    name: chem_administration
    description: List of chemical compounds administered to the host or site where
      sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
      include multiple compounds. For chemical entities of biological interest ontology
      (chebi) (v 163), http://purl.bioontology.org/ontology/chebi
    title: chemical administration
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{termLabel} [{termID}];{timestamp}'
    slot_uri: MIXS:0000751
    multivalued: true
    alias: chem_administration
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000555
    multivalued: true
    alias: chem_mutagen
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001040
    multivalued: true
    alias: climate_environment
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}|{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0001041
    multivalued: false
    alias: cult_root_med
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000556
    multivalued: true
    alias: fertilizer_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  fungicide_regm:
    name: fungicide_regm
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000557
    multivalued: true
    alias: fungicide_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    required: false
    recommended: false
  gaseous_environment:
    name: gaseous_environment
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000558
    multivalued: true
    alias: gaseous_environment
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000859
    multivalued: false
    alias: genetic_mod
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000559
    multivalued: true
    alias: gravity
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001043
    multivalued: false
    alias: growth_facil
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001044
    multivalued: false
    alias: growth_habit
    owner: MimarksSPlantAssociated
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    range: GROWTH_HABIT_ENUM
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000560
    multivalued: true
    alias: growth_hormone_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  herbicide_regm:
    name: herbicide_regm
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000561
    multivalued: true
    alias: herbicide_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    required: false
    recommended: false
  host_age:
    name: host_age
    description: Age of host at the time of sampling; relevant scale depends on species
      and study, e.g. Could be seconds for amoebae or centuries for trees
    title: host age
    examples:
    - value: 10 days
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000255
    multivalued: false
    alias: host_age
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_common_name:
    name: host_common_name
    description: Common name of the host
    title: host common name
    examples:
    - value: rice
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000248
    multivalued: false
    alias: host_common_name
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  host_disease_stat:
    name: host_disease_stat
    description: List of diseases with which the host has been diagnosed; can include
      multiple diagnoses. The value of the field depends on host; for humans the terms
      should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
      non-human host diseases are free text
    title: host disease status
    examples:
    - value: downy mildew
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000031
    multivalued: false
    alias: host_disease_stat
    owner: MimarksSPlantAssociated
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000257
    multivalued: false
    alias: host_dry_mass
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_genotype:
    name: host_genotype
    description: Observed genotype
    title: host genotype
    examples:
    - value: Ts
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000365
    multivalued: false
    alias: host_genotype
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  host_height:
    name: host_height
    description: The height of subject
    title: host height
    examples:
    - value: 1 meter
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000264
    multivalued: false
    alias: host_height
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_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-6-2-rc/mixs_6_2_rc
    string_serialization: '{rank name}:{text}'
    slot_uri: MIXS:0001318
    multivalued: true
    alias: host_subspecf_genlin
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    range: string
    required: false
    recommended: false
  host_length:
    name: host_length
    description: The length of subject
    title: host length
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000256
    multivalued: false
    alias: host_length
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_life_stage:
    name: host_life_stage
    description: Description of life stage of host
    title: host life stage
    examples:
    - value: adult
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000251
    multivalued: false
    alias: host_life_stage
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  host_phenotype:
    name: host_phenotype
    description: Phenotype of human or other host. Use terms from the phenotypic quality
      ontology (pato) or the Human Phenotype Ontology (HP)
    title: host phenotype
    examples:
    - value: seed pod; green [PATO:0000320]
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000874
    multivalued: false
    alias: host_phenotype
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  host_taxid:
    name: host_taxid
    description: NCBI taxon id of the host, e.g. 9606
    title: host taxid
    examples:
    - value: '4530'
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{NCBI taxid}'
    slot_uri: MIXS:0000250
    multivalued: false
    alias: host_taxid
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
  host_tot_mass:
    name: host_tot_mass
    description: Total mass of the host at collection, the unit depends on host
    title: host total mass
    examples:
    - value: 2500 gram
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000263
    multivalued: false
    alias: host_tot_mass
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000567
    multivalued: false
    alias: host_wet_mass
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000568
    multivalued: true
    alias: humidity_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};{float} {unit}'
    slot_uri: MIXS:0000569
    multivalued: false
    alias: light_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0001052
    multivalued: true
    alias: mechanical_damage
    owner: MimarksSPlantAssociated
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000570
    multivalued: true
    alias: mineral_nutr_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  misc_param:
    name: misc_param
    annotations:
      Expected_value:
        tag: Expected_value
        value: parameter name;measurement value
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    examples:
    - value: Bicarbonate ion concentration;2075 micromole per kilogram
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    multivalued: true
    alias: misc_param
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  non_min_nutr_regm:
    name: non_min_nutr_regm
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000571
    multivalued: true
    alias: non_min_nutr_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    required: false
    recommended: false
  organism_count:
    name: organism_count
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
    slot_uri: MIXS:0000103
    multivalued: true
    alias: organism_count
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  oxy_stat_samp:
    name: oxy_stat_samp
    description: Oxygenation status of sample
    title: oxygenation status of sample
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000753
    multivalued: false
    alias: oxy_stat_samp
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - Air
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: OXY_STAT_SAMP_ENUM
    required: false
    recommended: false
  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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{float};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001056
    multivalued: true
    alias: ph_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    required: false
    recommended: false
  perturbation:
    name: perturbation
    description: Type of perturbation, e.g. chemical administration, physical disturbance,
      etc., coupled with perturbation regimen including how many times the perturbation
      was repeated, how long each perturbation lasted, and the start and end time
      of the entire perturbation period; can include multiple perturbation types
    title: perturbation
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000754
    multivalued: true
    alias: perturbation
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  pesticide_regm:
    name: pesticide_regm
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000573
    multivalued: true
    alias: pesticide_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    required: false
    recommended: false
  plant_growth_med:
    name: plant_growth_med
    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-6-2-rc/mixs_6_2_rc
    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
    multivalued: false
    alias: plant_growth_med
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
    required: false
    recommended: false
  plant_product:
    name: plant_product
    description: Substance produced by the plant, where the sample was obtained from
    title: plant product
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0001058
    multivalued: false
    alias: plant_product
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001059
    multivalued: false
    alias: plant_sex
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: PLANT_SEX_ENUM
    required: false
    recommended: false
  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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001060
    multivalued: false
    alias: plant_struc
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    required: false
    recommended: false
    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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000575
    multivalued: true
    alias: radiation_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000576
    multivalued: true
    alias: rainfall_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001061
    multivalued: false
    alias: root_cond
    owner: MimarksSPlantAssociated
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
    required: false
    recommended: false
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000577
    multivalued: false
    alias: root_med_carbon
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000578
    multivalued: false
    alias: root_med_macronutr
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000579
    multivalued: false
    alias: root_med_micronutr
    owner: MimarksSPlantAssociated
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000580
    multivalued: false
    alias: root_med_suppl
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001062
    multivalued: false
    alias: root_med_ph
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - PlantAssociated
    range: float
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000581
    multivalued: false
    alias: root_med_regl
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001063
    multivalued: false
    alias: root_med_solid
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
  salt_regm:
    name: salt_regm
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000582
    multivalued: true
    alias: salt_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000860
    multivalued: false
    alias: samp_capt_status
    owner: MimarksSPlantAssociated
    domain_of:
    - HostAssociated
    - PlantAssociated
    range: SAMP_CAPT_STATUS_ENUM
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000249
    multivalued: false
    alias: samp_dis_stage
    owner: MimarksSPlantAssociated
    domain_of:
    - HostAssociated
    - PlantAssociated
    range: SAMP_DIS_STAGE_ENUM
    required: false
    recommended: false
  salinity:
    name: salinity
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: practical salinity unit, percentage
    description: The total concentration of all dissolved salts in a liquid or solid
      sample. While salinity can be measured by a complete chemical analysis, this
      method is difficult and time consuming. More often, it is instead derived from
      the conductivity measurement. This is known as practical salinity. These derivations
      compare the specific conductance of the sample to a salinity standard such as
      seawater
    title: salinity
    examples:
    - value: 25 practical salinity unit
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000183
    multivalued: false
    alias: salinity
    owner: MimarksSPlantAssociated
    domain_of:
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_store_dur:
    name: samp_store_dur
    description: Duration for which the sample was stored. Indicate the duration for
      which the sample was stored written in ISO 8601 format
    title: sample storage duration
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000116
    multivalued: false
    alias: samp_store_dur
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
    structured_pattern:
      syntax: ^{duration}$
      interpolated: true
      partial_match: true
  samp_store_loc:
    name: samp_store_loc
    description: Location at which sample was stored, usually name of a specific freezer/room
    title: sample storage location
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000755
    multivalued: false
    alias: samp_store_loc
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  samp_store_temp:
    name: samp_store_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature at which sample was stored, e.g. -80 degree Celsius
    title: sample storage temperature
    examples:
    - value: -80 degree Celsius
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000110
    multivalued: false
    alias: samp_store_temp
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001068
    multivalued: true
    alias: season_environment
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001069
    multivalued: true
    alias: standing_water_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001070
    multivalued: false
    alias: tiss_cult_growth_med
    owner: MimarksSPlantAssociated
    domain_of:
    - PlantAssociated
    range: string
    required: false
    recommended: false
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: true
  water_temp_regm:
    name: water_temp_regm
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000590
    multivalued: true
    alias: water_temp_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    required: false
    recommended: false
  watering_regm:
    name: watering_regm
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000591
    multivalued: true
    alias: watering_regm
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - PlantAssociated
    range: string
    required: false
    recommended: false
  host_symbiont:
    name: host_symbiont
    description: The taxonomic name of the organism(s) found living in mutualistic,
      commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont
      can have its own symbionts. For example, parasites may have hyperparasites (=parasites
      of the parasite)
    title: observed host symbionts
    examples:
    - value: flukeworms
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0001298
    multivalued: true
    alias: host_symbiont
    owner: MimarksSPlantAssociated
    domain_of:
    - Agriculture
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    required: false
    recommended: false
class_uri: MIXS:0010008_0016010