Combination: Mimag combined with FoodFarmEnvironment (MimagFoodFarmEnvironment)

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

Composition

Mimag [Checklist] + FoodFarmEnvironment [Extension]

Terms

MIXS ID	Name	Cardinality and Range	Description
MIXS:0001107	samp_name	1 String	A local identifier or name that for the material sample used for extracting n...
MIXS:0000017	size_frac	0..1 String	Filtering pore size used in sample preparation
MIXS:0000043	lib_screen	0..1 recommended String	Specific enrichment or screening methods applied before and/or after creating...
MIXS:0000062	ref_db	0..1 String	List of database(s) used for ORF annotation, along with version number and re...
MIXS:0000038	nucl_acid_amp	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...
MIXS:0000039	lib_size	0..1 recommended Integer	Total number of clones in the library prepared for the project
MIXS:0000005	contam_screen_input	0..1 ContamScreenInputEnum	The type of sequence data used as input
MIXS:0000047	mid	0..1 recommended String	Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe...
MIXS:0000057	assembly_name	0..1 recommended String	Name/version of the assembly provided by the submitter that is used in the ge...
MIXS:0000113	temp	0..1 recommended String	Temperature of the sample at the time of sampling
MIXS:0000069	compl_score	1 String	Completeness score is typically based on either the fraction of markers found...
MIXS:0000067	trnas	0..1 String	The total number of tRNAs identified from the SAG or MAG
MIXS:0000080	mag_cov_software	0..1 MagCovSoftwareEnum	Tool(s) used to determine the genome coverage if coverage is used as a binnin...
MIXS:0000037	nucl_acid_ext	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...
MIXS:0000001	samp_size	0..1 recommended String	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...
MIXS:0000094	alt	0..1 recommended String	Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba...
MIXS:0000077	bin_param	1 BinParamEnum	The parameters that have been applied during the extraction of genomes from m...
MIXS:0000078	bin_software	1 String	Tool(s) used for the extraction of genomes from metagenomic datasets, where p...
MIXS:0000026	source_mat_id	* recommended String	A unique identifier assigned to a material sample (as defined by http://rs
MIXS:0000111	samp_vol_we_dna_ext	0..1 String	Volume (ml) or mass (g) of total collected sample processed for DNA extractio...
MIXS:0000040	lib_reads_seqd	0..1 recommended Integer	Total number of clones sequenced from the library
MIXS:0000015	rel_to_oxygen	0..1 RelToOxygenEnum	Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ...
MIXS:0000079	reassembly_bin	0..1 Boolean	Has an assembly been performed on a genome bin extracted from a metagenomic a...
MIXS:0000074	decontam_software	0..1 String	Tool(s) used in contamination screening
MIXS:0000002	samp_collect_device	0..1 recommended String	The device used to collect an environmental sample
MIXS:0000060	number_contig	0..1 Integer	Total number of contigs in the cleaned/submitted assembly that makes up a giv...
MIXS:0000068	trna_ext_software	0..1 String	Tools used for tRNA identification
MIXS:0000041	lib_layout	0..1 recommended LibLayoutEnum	Specify whether to expect single, paired, or other configuration of reads
MIXS:0000073	contam_screen_param	0..1 String	Specific parameters used in the decontamination sofware, such as reference da...
MIXS:0000056	assembly_qual	1 AssemblyQualEnum	The assembly quality category is based on sets of criteria outlined for each ...
MIXS:0000025	ref_biomaterial	0..1 String	Primary publication if isolated before genome publication; otherwise, primary...
MIXS:0000092	project_name	1 String	Name of the project within which the sequencing was organized
MIXS:0000042	lib_vector	0..1 recommended String	Cloning vector type(s) used in construction of libraries
MIXS:0000048	adapters	0..1 recommended String	Adapters provide priming sequences for both amplification and sequencing of t...
MIXS:0001321	neg_cont_type	0..1 recommended NegContTypeEnum	The substance or equipment used as a negative control in an investigation
MIXS:0000058	assembly_software	1 String	Tool(s) used for assembly, including version number and parameters
MIXS:0000053	tax_ident	1 TaxIdentEnum	The phylogenetic marker(s) used to assign an organism name to the SAG or MAG
MIXS:0000072	contam_score	1 Float	The contamination score is based on the fraction of single-copy genes that ar...
MIXS:0000059	annot	0..1 String	Tool used for annotation, or for cases where annotation was provided by a com...
MIXS:0000066	x16s_recover_software	0..1 String	Tools used for 16S rRNA gene extraction
MIXS:0000065	x16s_recover	0..1 Boolean	Can a 16S gene be recovered from the submitted SAG or MAG?
MIXS:0001322	pos_cont_type	0..1 recommended String	The substance, mixture, product, or apparatus used to verify that a process w...
MIXS:0000061	feat_pred	0..1 String	Method used to predict UViGs features such as ORFs, integration site, etc
MIXS:0000070	compl_software	1 String	Tools used for completion estimate, i
MIXS:0000013	env_local_scale	1 String	Report the entity or entities which are in the sample or specimen s local vic...
MIXS:0000016	samp_mat_process	0..1 recommended String	A brief description of any processing applied to the sample during or after r...
MIXS:0000063	sim_search_meth	0..1 String	Tool used to compare ORFs with database, along with version and cutoffs used
MIXS:0000018	depth	1 recommended String	The vertical distance below local surface
MIXS:0001225	samp_collect_method	0..1 recommended String	The method employed for collecting the sample
MIXS:0000071	compl_appr	0..1 ComplApprEnum	The approach used to determine the completeness of a given genomic assembly, ...
MIXS:0000014	env_medium	1 String	Report the environmental material(s) immediately surrounding the sample or sp...
MIXS:0001320	samp_taxon_id	1 String	NCBI taxon id of the sample
MIXS:0000010	geo_loc_name	1 String	The geographical origin of the sample as defined by the country or sea name f...
MIXS:0000011	collection_date	1 Datetime	The time of sampling, either as an instance (single point in time) or interva...
MIXS:0000050	seq_meth	1 String	Sequencing machine used
MIXS:0000009	lat_lon	1 String	The geographical origin of the sample as defined by latitude and longitude
MIXS:0000093	elev	0..1 recommended String	Elevation of the sampling site is its height above a fixed reference point, m...
MIXS:0000012	env_broad_scale	1 String	Report the major environmental system the sample or specimen came from
MIXS:0000064	tax_class	0..1 String	Method used for taxonomic classification, along with reference database used,...
MIXS:0000008	experimental_factor	* recommended String	Variable aspects of an experiment design that can be used to describe an expe...
MIXS:0000091	associated_resource	* recommended String	A related resource that is referenced, cited, or otherwise associated to the ...
MIXS:0000090	sop	* recommended String	Standard operating procedures used in assembly and/or annotation of genomes, ...
MIXS:0000100	humidity	0..1 String	Amount of water vapour in the air, at the time of sampling
MIXS:0000103	organism_count	* String	Total cell count of any organism (or group of organisms) per gram, volume or ...
MIXS:0001335	spikein_count	0..1 String	Total cell count of any organism (or group of organisms) per gram, volume or ...
MIXS:0000110	samp_store_temp	0..1 String	Temperature at which sample was stored, e
MIXS:0000112	solar_irradiance	* String	The amount of solar energy that arrives at a specific area of a surface durin...
MIXS:0000114	ventilation_rate	0..1 String	Ventilation rate of the system in the sampled premises
MIXS:0000116	samp_store_dur	0..1 String	Duration for which the sample was stored
MIXS:0000118	wind_speed	0..1 String	speed of wind measured at the time of sampling
MIXS:0000183	salinity	0..1 String	The total concentration of all dissolved salts in a liquid or solid sample
MIXS:0000315	previous_land_use	0..1 String	Previous land use and dates
MIXS:0000318	crop_rotation	0..1 String	Whether or not crop is rotated, and if yes, rotation schedule
MIXS:0000334	soil_type_meth	0..1 String	Reference or method used in determining soil series name or other lower-level...
MIXS:0000337	tot_org_c_meth	0..1 String	Reference or method used in determining total organic carbon
MIXS:0000338	tot_nitro_cont_meth	0..1 String	Reference or method used in determining the total nitrogen
MIXS:0000255	host_age	0..1 String	Age of host at the time of sampling; relevant scale depends on species and st...
MIXS:0000257	host_dry_mass	0..1 String	Measurement of dry mass
MIXS:0000264	host_height	0..1 String	The height of subject
MIXS:0000256	host_length	0..1 String	The length of subject
MIXS:0000263	host_tot_mass	0..1 String	Total mass of the host at collection, the unit depends on host
MIXS:0000577	root_med_carbon	0..1 String	Source of organic carbon in the culture rooting medium; e
MIXS:0000578	root_med_macronutr	0..1 String	Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);...
MIXS:0000579	root_med_micronutr	0..1 String	Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, ...
MIXS:0000643	season_temp	0..1 String	Mean seasonal temperature
MIXS:0000645	season_precpt	0..1 String	The average of all seasonal precipitation values known, or an estimated equiv...
MIXS:0000533	tot_org_carb	0..1 String	Total organic carbon content
MIXS:0000530	tot_nitro_content	0..1 String	Total nitrogen content of the sample
MIXS:0000692	conduc	0..1 String	Electrical conductivity of water
MIXS:0000191	turbidity	0..1 String	Measure of the amount of cloudiness or haziness in water caused by individual...
MIXS:0000735	size_frac_low	0..1 String	Refers to the mesh/pore size used to pre-filter/pre-sort the sample
MIXS:0000736	size_frac_up	0..1 String	Mesh or pore size of the device used to retain the sample
MIXS:0000756	ventilation_type	* String	Ventilation system used in the sampled premises
MIXS:0000757	wind_direction	0..1 String	Wind direction is the direction from which a wind originates
MIXS:0000859	genetic_mod	0..1 String	Genetic modifications of the genome of an organism, which may occur naturally...
MIXS:0000874	host_phenotype	0..1 String	Phenotype of human or other host
MIXS:0001001	ph	0..1 Float	Ph measurement of the sample, or liquid portion of sample, or aqueous phase o...
MIXS:0000247	ances_data	0..1 String	Information about either pedigree or other ancestral information description ...
MIXS:0001038	biotic_regm	1..* String	Information about treatment(s) involving use of biotic factors, such as bacte...
MIXS:0000751	chem_administration	1..* String	List of chemical compounds administered to the host or site where sampling oc...
MIXS:0001044	growth_habit	0..1 GrowthHabitEnum	Characteristic shape, appearance or growth form of a plant species
MIXS:0000031	host_disease_stat	0..1 recommended String	List of diseases with which the host has been diagnosed; can include multiple...
MIXS:0000365	host_genotype	0..1 String	Observed genotype
MIXS:0000250	host_taxid	0..1 String	NCBI taxon id of the host, e
MIXS:0001052	mechanical_damage	* String	Information about any mechanical damage exerted on the plant; can include mul...
MIXS:0000754	perturbation	* String	Type of perturbation, e
MIXS:0001061	root_cond	0..1 String	Relevant rooting conditions such as field plot size, sowing density, containe...
MIXS:0001062	root_med_ph	0..1 Float	pH measurement of the culture rooting medium; e
MIXS:0001081	tillage	* TillageEnum	Note method(s) used for tilling
MIXS:0001106	ph_meth	0..1 String	Reference or method used in determining pH
MIXS:0001108	growth_medium	0..1 String	A liquid or gel containing nutrients, salts, and other factors formulated to ...
MIXS:0000829	season	0..1 String	The season when sampling occurred
MIXS:0001184	food_product_type	1 String	A food product type is a class of food products that is differentiated by its...
MIXS:0000998	samp_type	1 String	The type of material from which the sample was obtained
MIXS:0001110	farm_water_source	0..1 recommended FarmWaterSourceEnum	Source of water used on the farm for irrigation of crops or watering of lives...
MIXS:0001111	plant_water_method	0..1 recommended String	Description of the equipment or method used to distribute water to crops
MIXS:0000108	air_PM_concen	* String	Concentration of substances that remain suspended in the air, and comprise mi...
MIXS:0001113	animal_feed_equip	* String	Description of the feeding equipment used for livestock
MIXS:0001114	animal_intrusion	* String	Identification of animals intruding on the sample or sample site including in...
MIXS:0001115	anim_water_method	* String	Description of the equipment or method used to distribute water to livestock
MIXS:0001116	crop_yield	0..1 String	Amount of crop produced per unit or area of land
MIXS:0001117	cult_result	0..1 CultResultEnum	Any result of a bacterial culture experiment reported as a binary assessment ...
MIXS:0001118	cult_result_org	* String	Taxonomic information about the cultured organism(s)
MIXS:0001119	cult_target	* String	The target microbial analyte in terms of investigation scope
MIXS:0001120	plant_part_maturity	0..1 String	A description of the stage of development of a plant or plant part based on m...
MIXS:0001121	adjacent_environment	* String	Description of the environmental system or features that are adjacent to the ...
MIXS:0001122	water_source_adjac	* String	Description of the environmental features that are adjacent to the farm water...
MIXS:0001123	farm_equip_shared	* String	List of planting, growing or harvesting equipment shared with other farms
MIXS:0001124	farm_equip_san	* String	Method used to sanitize growing and harvesting equipment
MIXS:0001125	farm_equip_san_freq	0..1 String	The number of times farm equipment is cleaned
MIXS:0001126	farm_equip	* String	List of equipment used for planting, fertilization, harvesting, irrigation, l...
MIXS:0001127	fertilizer_admin	0..1 String	Type of fertilizer or amendment added to the soil or water for the purpose of...
MIXS:0001128	fertilizer_date	0..1 Datetime	Date of administration of soil amendment or fertilizer
MIXS:0001129	animal_group_size	0..1 Integer	The number of food animals of the same species that are maintained together a...
MIXS:0001130	animal_diet	* String	If the isolate is from a food animal, the type of diet eaten by the food anim...
MIXS:0001131	food_contact_surf	* String	The specific container or coating materials in direct contact with the food
MIXS:0001132	food_contain_wrap	0..1 String	Type of container or wrapping defined by the main container material, the con...
MIXS:0001133	food_harvest_proc	* String	A harvesting process is a process which takes in some food material from an i...
MIXS:0001134	food_pack_medium	* String	The medium in which the food is packed for preservation and handling or the m...
MIXS:0001135	food_preserv_proc	* String	The methods contributing to the prevention or retardation of microbial, enzym...
MIXS:0001136	food_prod_char	* String	Descriptors of the food production system such as wild caught, free-range, or...
MIXS:prod_label_claims	prod_label_claims	* String	Labeling claims containing descriptors such as wild caught, free-range, organ...
MIXS:0001137	food_trav_mode	* String	A descriptor for the method of movement of food commodity along the food dist...
MIXS:0001138	food_trav_vehic	* String	A descriptor for the mobile machine which is used to transport food commoditi...
MIXS:0001139	food_source	0..1 String	Type of plant or animal from which the food product or its major ingredient i...
MIXS:0001140	food_treat_proc	* String	Used to specifically characterize a food product based on the treatment or pr...
MIXS:0001141	extr_weather_event	* ExtrWeatherEventEnum	Unusual weather events that may have affected microbial populations
MIXS:0001142	date_extr_weath	* Datetime	Date of unusual weather events that may have affected microbial populations
MIXS:0001318	host_subspecf_genlin	* String	Information about the genetic distinctness of the host organism below the sub...
MIXS:0001144	intended_consumer	* String	Food consumer type, human or animal, for which the food product is produced a...
MIXS:0001145	library_prep_kit	0..1 String	Packaged kits (containing adapters, indexes, enzymes, buffers etc
MIXS:0001146	air_flow_impede	* String	Presence of objects in the area that would influence or impede air flow throu...
MIXS:0001147	lot_number	* String	A distinctive alpha-numeric identification code assigned by the manufacturer ...
MIXS:0001148	season_humidity	0..1 Float	Average humidity of the region throughout the growing season
MIXS:0001149	part_plant_animal	* String	The anatomical part of the organism being involved in food production or cons...
MIXS:0001057	plant_growth_med	0..1 String	Specification of the media for growing the plants or tissue cultured samples,...
MIXS:0001150	plant_reprod_crop	* PlantReprodCropEnum	Plant reproductive part used in the field during planting to start the crop
MIXS:0001151	samp_purpose	0..1 String	The reason that the sample was collected
MIXS:0001152	repository_name	* String	The name of the institution where the sample or DNA extract is held or "sampl...
MIXS:0001153	samp_pooling	* String	Physical combination of several instances of like material, e
MIXS:0001154	samp_source_mat_cat	0..1 String	This is the scientific role or category that the subject organism or material...
MIXS:0001155	sequencing_kit	0..1 String	Pre-filled, ready-to-use reagent cartridges
MIXS:0001156	sequencing_location	0..1 String	The location the sequencing run was performed
MIXS:0001157	serovar_or_serotype	* String	A characterization of a cell or microorganism based on the antigenic properti...
MIXS:0001158	soil_conductivity	0..1 String	Conductivity of soil at time of sampling
MIXS:0001159	soil_cover	0..1 String	Material covering the sampled soil
MIXS:0001160	soil_pH	0..1 Float	The pH of soil at time of sampling
MIXS:0001161	rel_location	0..1 String	Location of sampled soil to other parts of the farm e
MIXS:0001162	soil_porosity	0..1 String	Porosity of soil or deposited sediment is volume of voids divided by the tota...
MIXS:0001163	soil_temp	0..1 String	Temperature of soil at the time of sampling
MIXS:0001164	soil_texture_class	0..1 SoilTextureClassEnum	One of the 12 soil texture classes use to describe soil texture based on the ...
MIXS:0000336	soil_texture_meth	0..1 String	Reference or method used in determining soil texture
MIXS:0000332	soil_type	0..1 String	Description of the soil type or classification
MIXS:0001167	spikein_org	* String	Taxonomic information about the spike-in organism(s)
MIXS:0001168	spikein_serovar	* String	Taxonomic information about the spike-in organism(s) at the serovar or seroty...
MIXS:0001169	spikein_growth_med	* String	A liquid or gel containing nutrients, salts, and other factors formulated to ...
MIXS:0001170	spikein_strain	* String	Taxonomic information about the spike-in organism(s) at the strain level
MIXS:0001171	spikein_antibiotic	* String	Antimicrobials used in research study to assess effects of exposure on microb...
MIXS:0001172	spikein_metal	* String	Heavy metals used in research study to assess effects of exposure on microbio...
MIXS:0001173	timepoint	0..1 String	Time point at which a sample or observation is made or taken from a biomateri...
MIXS:0001174	water_frequency	0..1 String	Number of water delivery events within a given period of time
MIXS:0001175	water_pH	0..1 Float	pH measurement of the sample, or liquid portion of sample, or aqueous phase o...
MIXS:0001176	water_source_shared	* String	Other users sharing access to the same water source
MIXS:0001177	enrichment_protocol	0..1 String	The microbiological workflow or protocol followed to test for the presence or...
MIXS:0001178	food_quality_date	0..1 String	The date recommended for the use of the product while at peak quality, this d...
MIXS:0001179	IFSAC_category	1..* String	The IFSAC food categorization scheme has five distinct levels to which foods ...
MIXS:0001180	animal_housing	* String	Description of the housing system of the livestock
MIXS:0001181	cult_isol_date	0..1 Datetime	The datetime marking the end of a process in which a sample yields a positive...
MIXS:0001182	food_clean_proc	0..1 FoodCleanProcEnum	The process of cleaning food to separate other environmental materials from t...
MIXS:0000752	misc_param	* String	Any other measurement performed or parameter collected, that is not listed he...

LinkML Source

Direct

name: MimagFoodFarmEnvironment
description: MIxS Data that comply with the Mimag checklist and the FoodFarmEnvironment
  Extension
title: Mimag combined with FoodFarmEnvironment
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: FoodFarmEnvironment
mixins:
- Mimag
class_uri: MIXS:0010011_0016020

Induced

name: MimagFoodFarmEnvironment
description: MIxS Data that comply with the Mimag checklist and the FoodFarmEnvironment
  Extension
title: Mimag combined with FoodFarmEnvironment
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: FoodFarmEnvironment
mixins:
- Mimag
attributes:
  samp_name:
    name: samp_name
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ''
    description: A local identifier or name that for the material sample used for
      extracting nucleic acids, and subsequent sequencing. It can refer either to
      the original material collected or to any derived sub-samples. It can have any
      format, but we suggest that you make it concise, unique and consistent within
      your lab, and as informative as possible. INSDC requires every sample name from
      a single Submitter to be unique. Use of a globally unique identifier for the
      field source_mat_id is recommended in addition to sample_name
    title: sample name
    examples:
    - value: ISDsoil1
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    slot_uri: MIXS:0001107
    alias: samp_name
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: true
  size_frac:
    name: size_frac
    annotations:
      Expected_value:
        tag: Expected_value
        value: filter size value range
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    examples:
    - value: 0-0.22 micrometer
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - fraction
    - size
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    alias: size_frac
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
  lib_screen:
    name: lib_screen
    annotations:
      Expected_value:
        tag: Expected_value
        value: screening strategy name
    description: Specific enrichment or screening methods applied before and/or after
      creating libraries
    title: library screening strategy
    examples:
    - value: enriched, screened, normalized
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000043
    alias: lib_screen
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  ref_db:
    name: ref_db
    annotations:
      Expected_value:
        tag: Expected_value
        value: names, versions, and references of databases
    description: List of database(s) used for ORF annotation, along with version number
      and reference to website or publication
    title: reference database(s)
    examples:
    - value: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017
        doi:10.1093/nar/gkw975
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - database
    string_serialization: '{database};{version};{reference}'
    slot_uri: MIXS:0000062
    alias: ref_db
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
  nucl_acid_amp:
    name: nucl_acid_amp
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the enzymatic amplification (PCR,
      TMA, NASBA) of specific nucleic acids
    title: nucleic acid amplification
    examples:
    - value: https://phylogenomics.me/protocols/16s-pcr-protocol/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000038
    alias: nucl_acid_amp
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  lib_size:
    name: lib_size
    description: Total number of clones in the library prepared for the project
    title: library size
    examples:
    - value: '50'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    - size
    slot_uri: MIXS:0000039
    alias: lib_size
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    recommended: true
  contam_screen_input:
    name: contam_screen_input
    description: The type of sequence data used as input
    title: contamination screening input
    examples:
    - value: contigs
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000005
    alias: contam_screen_input
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - Misag
    range: ContamScreenInputEnum
  mid:
    name: mid
    description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
      used to specifically tag unique samples in a sequencing run. Sequence should
      be reported in uppercase letters
    title: multiplex identifiers
    examples:
    - value: GTGAATAT
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - identifier
    slot_uri: MIXS:0000047
    alias: mid
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^[ACGTRKSYMWBHDVN]+$
    structured_pattern:
      syntax: ^{ambiguous_nucleotides}$
      interpolated: true
      partial_match: true
  assembly_name:
    name: assembly_name
    annotations:
      Expected_value:
        tag: Expected_value
        value: name and version of assembly
    description: Name/version of the assembly provided by the submitter that is used
      in the genome browsers and in the community
    title: assembly name
    examples:
    - value: HuRef, JCVI_ISG_i3_1.0
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    string_serialization: '{text} {text}'
    slot_uri: MIXS:0000057
    alias: assembly_name
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  temp:
    name: temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature of the sample at the time of sampling
    title: temperature
    examples:
    - value: 25 degree Celsius
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - temperature
    slot_uri: MIXS:0000113
    alias: temp
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  compl_score:
    name: compl_score
    annotations:
      Expected_value:
        tag: Expected_value
        value: quality;percent completeness
    description: 'Completeness score is typically based on either the fraction of
      markers found as compared to a database or the percent of a genome found as
      compared to a closely related reference genome. High Quality Draft: >90%, Medium
      Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated
      completeness scores'
    title: completeness score
    examples:
    - value: med;60%
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - score
    string_serialization: '[high|med|low];{percentage}'
    slot_uri: MIXS:0000069
    alias: compl_score
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: string
    required: true
  trnas:
    name: trnas
    annotations:
      Expected_value:
        tag: Expected_value
        value: value from 0-21
    description: The total number of tRNAs identified from the SAG or MAG
    title: number of standard tRNAs extracted
    examples:
    - value: '18'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - number
    string_serialization: '{integer}'
    slot_uri: MIXS:0000067
    alias: trnas
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - Misag
    - Miuvig
    range: string
  mag_cov_software:
    name: mag_cov_software
    description: Tool(s) used to determine the genome coverage if coverage is used
      as a binning parameter in the extraction of genomes from metagenomic datasets
    title: MAG coverage software
    examples:
    - value: bbmap
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    slot_uri: MIXS:0000080
    alias: mag_cov_software
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - Miuvig
    range: MagCovSoftwareEnum
  nucl_acid_ext:
    name: nucl_acid_ext
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the material separation to recover
      the nucleic acid fraction from a sample
    title: nucleic acid extraction
    examples:
    - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000037
    alias: nucl_acid_ext
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  samp_size:
    name: samp_size
    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
      sample collected
    title: amount or size of sample collected
    examples:
    - value: 5 liter
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - size
    slot_uri: MIXS:0000001
    alias: samp_size
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  alt:
    name: alt
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric
      balloons and heights of places such as atmospheric layers and clouds. It is
      used to measure the height of an object which is above the earth's surface.
      In this context, the altitude measurement is the vertical distance between the
      earth's surface above sea level and the sampled position in the air
    title: altitude
    examples:
    - value: 100 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000094
    alias: alt
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - HostAssociated
    - MiscellaneousNaturalOrArtificialEnvironment
    - SymbiontAssociated
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  bin_param:
    name: bin_param
    description: The parameters that have been applied during the extraction of genomes
      from metagenomic datasets
    title: binning parameters
    examples:
    - value: coverage
      description: was 'coverage and kmer'
    - value: kmer
      description: was coverage and kmer
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - parameter
    slot_uri: MIXS:0000077
    alias: bin_param
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - Miuvig
    range: BinParamEnum
    required: true
  bin_software:
    name: bin_software
    annotations:
      Expected_value:
        tag: Expected_value
        value: names and versions of software(s) used
    description: Tool(s) used for the extraction of genomes from metagenomic datasets,
      where possible include a product ID (PID) of the tool(s) used
    title: binning software
    examples:
    - value: MetaCluster-TA (RRID:SCR_004599), MaxBin (biotools:maxbin)
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    string_serialization: '{software};{version}{PID}'
    slot_uri: MIXS:0000078
    alias: bin_software
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - Miuvig
    range: string
    required: true
  source_mat_id:
    name: source_mat_id
    annotations:
      Expected_value:
        tag: Expected_value
        value: 'for cultures of microorganisms: identifiers for two culture collections;
          for other material a unique arbitrary identifer'
    description: A unique identifier assigned to a material sample (as defined by
      http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
      digital record of a material sample) used for extracting nucleic acids, and
      subsequent sequencing. The identifier can refer either to the original material
      collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
      /bio_material, or /culture_collection may or may not share the same value as
      the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
      may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
      sampled tissue with the same identifier. However, the /culture_collection qualifier
      may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
      would refer to an identifier from some derived culture from which the nucleic
      acids were extracted (e.g. xatc123 or ark:/2154/R2)
    title: source material identifiers
    examples:
    - value: MPI012345
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - identifier
    - material
    - source
    slot_uri: MIXS:0000026
    alias: source_mat_id
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - SymbiontAssociated
    range: string
    recommended: true
    multivalued: true
  samp_vol_we_dna_ext:
    name: samp_vol_we_dna_ext
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milliliter, gram, milligram, square centimeter
    description: 'Volume (ml) or mass (g) of total collected sample processed for
      DNA extraction. Note: total sample collected should be entered under the term
      Sample Size (MIXS:0000001)'
    title: sample volume or weight for DNA extraction
    examples:
    - value: 1500 milliliter
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - dna
    - sample
    - volume
    - weight
    slot_uri: MIXS:0000111
    alias: samp_vol_we_dna_ext
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  lib_reads_seqd:
    name: lib_reads_seqd
    description: Total number of clones sequenced from the library
    title: library reads sequenced
    examples:
    - value: '20'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000040
    alias: lib_reads_seqd
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    recommended: true
  rel_to_oxygen:
    name: rel_to_oxygen
    description: Is this organism an aerobe, anaerobe? Please note that aerobic and
      anaerobic are valid descriptors for microbial environments
    title: relationship to oxygen
    examples:
    - value: aerobe
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - oxygen
    - relationship
    slot_uri: MIXS:0000015
    alias: rel_to_oxygen
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    range: RelToOxygenEnum
  reassembly_bin:
    name: reassembly_bin
    description: Has an assembly been performed on a genome bin extracted from a metagenomic
      assembly?
    title: reassembly post binning
    examples:
    - value: 'no'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - post
    slot_uri: MIXS:0000079
    alias: reassembly_bin
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - Miuvig
    range: boolean
  decontam_software:
    name: decontam_software
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration
    description: Tool(s) used in contamination screening
    title: decontamination software
    examples:
    - value: anvi'o
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    string_serialization: '[checkm/refinem|anvi''o|prodege|bbtools:decontaminate.sh|acdc|combination]'
    slot_uri: MIXS:0000074
    alias: decontam_software
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - Misag
    range: string
  samp_collect_device:
    name: samp_collect_device
    annotations:
      Expected_value:
        tag: Expected_value
        value: device name
    description: The device used to collect an environmental sample. This field accepts
      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
    title: sample collection device
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - device
    - sample
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000002
    alias: samp_collect_device
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
  number_contig:
    name: number_contig
    description: Total number of contigs in the cleaned/submitted assembly that makes
      up a given genome, SAG, MAG, or UViG
    title: number of contigs
    examples:
    - value: '40'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - number
    slot_uri: MIXS:0000060
    alias: number_contig
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: integer
  trna_ext_software:
    name: trna_ext_software
    description: Tools used for tRNA identification
    title: tRNA extraction software
    examples:
    - value: infernal;v2;default parameters
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    slot_uri: MIXS:0000068
    alias: trna_ext_software
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - Misag
    - Miuvig
    range: string
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  lib_layout:
    name: lib_layout
    description: Specify whether to expect single, paired, or other configuration
      of reads
    title: library layout
    examples:
    - value: paired
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000041
    alias: lib_layout
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: LibLayoutEnum
    recommended: true
  contam_screen_param:
    name: contam_screen_param
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration;value or name
    description: Specific parameters used in the decontamination sofware, such as
      reference database, coverage, and kmers. Combinations of these parameters may
      also be used, i.e. kmer and coverage, or reference database and kmer
    title: contamination screening parameters
    examples:
    - value: kmer
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - parameter
    string_serialization: '[ref db|kmer|coverage|combination];{text|integer}'
    slot_uri: MIXS:0000073
    alias: contam_screen_param
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - Misag
    range: string
  assembly_qual:
    name: assembly_qual
    description: 'The assembly quality category is based on sets of criteria outlined
      for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
      contiguous sequence per replicon without gaps or ambiguities with a consensus
      error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
      where gaps span repetitive regions. Presence of the large subunit (LSU) RNA,
      small subunit (SSU) and the presence of 5.8S rRNA or 5S rRNA depending on whether
      it is a eukaryotic or prokaryotic genome, respectively. Medium Quality Draft:Many
      fragments with little to no review of assembly other than reporting of standard
      assembly statistics. Low Quality Draft:Many fragments with little to no review
      of assembly other than reporting of standard assembly statistics. Assembly statistics
      include, but are not limited to total assembly size, number of contigs, contig
      N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated,
      contiguous sequence per replicon without gaps or ambiguities, with extensive
      manual review and editing to annotate putative gene functions and transcriptional
      units. High-quality draft genome: One or multiple fragments, totaling   90%
      of the expected genome or replicon sequence or predicted complete. Genome fragment(s):
      One or multiple fragments, totalling < 90% of the expected genome or replicon
      sequence, or for which no genome size could be estimated'
    title: assembly quality
    examples:
    - value: High-quality draft genome
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - quality
    slot_uri: MIXS:0000056
    alias: assembly_qual
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: AssemblyQualEnum
    required: true
  ref_biomaterial:
    name: ref_biomaterial
    description: Primary publication if isolated before genome publication; otherwise,
      primary genome report
    title: reference for biomaterial
    examples:
    - value: doi:10.1016/j.syapm.2018.01.009
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000025
    alias: ref_biomaterial
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  project_name:
    name: project_name
    description: Name of the project within which the sequencing was organized
    title: project name
    examples:
    - value: Forest soil metagenome
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - project
    slot_uri: MIXS:0000092
    alias: project_name
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: true
  lib_vector:
    name: lib_vector
    annotations:
      Expected_value:
        tag: Expected_value
        value: vector
    description: Cloning vector type(s) used in construction of libraries
    title: library vector
    examples:
    - value: Bacteriophage P1
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000042
    alias: lib_vector
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  adapters:
    name: adapters
    description: Adapters provide priming sequences for both amplification and sequencing
      of the sample-library fragments. Both adapters should be reported; in uppercase
      letters
    title: adapters
    examples:
    - value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000048
    alias: adapters
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    structured_pattern:
      syntax: ^{adapter_A_DNA_sequence};{adapter_B_DNA_sequence}$
      interpolated: true
      partial_match: true
  neg_cont_type:
    name: neg_cont_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration or text
    description: The substance or equipment used as a negative control in an investigation
    title: negative control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - type
    slot_uri: MIXS:0001321
    alias: neg_cont_type
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: NegContTypeEnum
    recommended: true
  assembly_software:
    name: assembly_software
    description: Tool(s) used for assembly, including version number and parameters
    title: assembly software
    examples:
    - value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    slot_uri: MIXS:0000058
    alias: assembly_software
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  tax_ident:
    name: tax_ident
    description: The phylogenetic marker(s) used to assign an organism name to the
      SAG or MAG
    title: taxonomic identity marker
    examples:
    - value: other
      description: was other <colon> rpoB gene
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - identifier
    - marker
    - taxon
    slot_uri: MIXS:0000053
    alias: tax_ident
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: TaxIdentEnum
    required: true
  contam_score:
    name: contam_score
    description: 'The contamination score is based on the fraction of single-copy
      genes that are observed more than once in a query genome. The following scores
      are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low
      Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be
      deposited into any of the public databases'
    title: contamination score
    examples:
    - value: '0.01'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - score
    slot_uri: MIXS:0000072
    alias: contam_score
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - Misag
    range: float
    required: true
  annot:
    name: annot
    annotations:
      Expected_value:
        tag: Expected_value
        value: name of tool or pipeline used, or annotation source description
    description: Tool used for annotation, or for cases where annotation was provided
      by a community jamboree or model organism database rather than by a specific
      submitter
    title: annotation
    examples:
    - value: prokka
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000059
    alias: annot
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
  x16s_recover_software:
    name: x16s_recover_software
    description: Tools used for 16S rRNA gene extraction
    title: 16S recovery software
    examples:
    - value: rambl;v2;default parameters
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - recover
    - software
    slot_uri: MIXS:0000066
    alias: x16s_recover_software
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - Misag
    range: string
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  x16s_recover:
    name: x16s_recover
    description: Can a 16S gene be recovered from the submitted SAG or MAG?
    title: 16S recovered
    examples:
    - value: 'yes'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - recover
    slot_uri: MIXS:0000065
    alias: x16s_recover
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - Misag
    range: boolean
  pos_cont_type:
    name: pos_cont_type
    description: The substance, mixture, product, or apparatus used to verify that
      a process which is part of an investigation delivers a true positive
    title: positive control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - type
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    alias: pos_cont_type
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    recommended: true
  feat_pred:
    name: feat_pred
    description: Method used to predict UViGs features such as ORFs, integration site,
      etc
    title: feature prediction
    examples:
    - value: Prodigal;2.6.3;default parameters
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - feature
    - predict
    slot_uri: MIXS:0000061
    alias: feat_pred
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  compl_software:
    name: compl_software
    annotations:
      Expected_value:
        tag: Expected_value
        value: names and versions of software(s) used
    description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
    title: completeness software
    examples:
    - value: checkm
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    string_serialization: '{software};{version}'
    slot_uri: MIXS:0000070
    alias: compl_software
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: string
    required: true
  env_local_scale:
    name: env_local_scale
    annotations:
      Expected_value:
        tag: Expected_value
        value: Environmental entities having causal influences upon the entity at
          time of sampling
    description: 'Report the entity or entities which are in the sample or specimen
      s local vicinity and which you believe have significant causal influences on
      your sample or specimen. We recommend using EnvO terms which are of smaller
      spatial grain than your entry for env_broad_scale. Terms, such as anatomical
      sites, from other OBO Library ontologies which interoperate with EnvO (e.g.
      UBERON) are accepted in this field. EnvO documentation about how to use the
      field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: local environmental context
    examples:
    - value: hillside [ENVO:01000333]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - context
    - environmental
    slot_uri: MIXS:0000013
    alias: env_local_scale
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  samp_mat_process:
    name: samp_mat_process
    description: A brief description of any processing applied to the sample during
      or after retrieving the sample from environment, or a link to the relevant protocol(s)
      performed
    title: sample material processing
    examples:
    - value: filtering of seawater, storing samples in ethanol
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - material
    - process
    - sample
    slot_uri: MIXS:0000016
    alias: samp_mat_process
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  sim_search_meth:
    name: sim_search_meth
    description: Tool used to compare ORFs with database, along with version and cutoffs
      used
    title: similarity search method
    examples:
    - value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    slot_uri: MIXS:0000063
    alias: sim_search_meth
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  depth:
    name: depth
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: The vertical distance below local surface. For sediment or soil samples
      depth is measured from sediment or soil surface, respectively. Depth can be
      reported as an interval for subsurface samples
    title: depth
    examples:
    - value: 10 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - depth
    slot_uri: MIXS:0000018
    alias: depth
    owner: MimagFoodFarmEnvironment
    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
    required: true
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_collect_method:
    name: samp_collect_method
    description: The method employed for collecting the sample
    title: sample collection method
    examples:
    - value: swabbing
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    - sample
    slot_uri: MIXS:0001225
    alias: samp_collect_method
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: true
  compl_appr:
    name: compl_appr
    annotations:
      Expected_value:
        tag: Expected_value
        value: text
    description: The approach used to determine the completeness of a given genomic
      assembly, which would typically make use of a set of conserved marker genes
      or a closely related reference genome. For UViG completeness, include reference
      genome or group used, and contig feature suggesting a complete genome
    title: completeness approach
    examples:
    - value: other
      description: was other <colon> UViG length compared to the average length of
        reference genomes from the P22virus genus (NCBI RefSeq v83)
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000071
    alias: compl_appr
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Mimag
    - Misag
    - Miuvig
    range: ComplApprEnum
  env_medium:
    name: env_medium
    description: 'Report the environmental material(s) immediately surrounding the
      sample or specimen at the time of sampling. We recommend using subclasses of
      ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
      documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
      . Terms from other OBO ontologies are permissible as long as they reference
      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
      (e.g. a tree, a leaf, a table top)'
    title: environmental medium
    examples:
    - value: bluegrass field soil [ENVO:00005789]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - environmental
    slot_uri: MIXS:0000014
    alias: env_medium
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  samp_taxon_id:
    name: samp_taxon_id
    description: NCBI taxon id of the sample.  Maybe be a single taxon or mixed taxa
      sample. Use 'synthetic metagenome  for mock community/positive controls, or
      'blank sample' for negative controls
    title: taxonomy ID of DNA sample
    examples:
    - value: Gut Metagenome [NCBITaxon:749906]
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - dna
    - identifier
    - sample
    - taxon
    slot_uri: MIXS:0001320
    alias: samp_taxon_id
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$
    structured_pattern:
      syntax: ^{text} \[{NCBItaxon_id}\]$
      interpolated: true
      partial_match: true
  geo_loc_name:
    name: geo_loc_name
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name. Country or sea names should be chosen
      from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
      (http://purl.bioontology.org/ontology/GAZ)
    title: geographic location (country and/or sea,region)
    examples:
    - value: 'USA: Maryland, Bethesda'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - geographic
    - location
    slot_uri: MIXS:0000010
    alias: geo_loc_name
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: string
    required: true
    pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
    structured_pattern:
      syntax: '^{text}: {text}, {text}$'
      interpolated: true
      partial_match: true
  collection_date:
    name: collection_date
    description: 'The time of sampling, either as an instance (single point in time)
      or interval. In case no exact time is available, the date/time can be right
      truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
      2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
    title: collection date
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - date
    slot_uri: MIXS:0000011
    alias: collection_date
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: datetime
    required: true
  seq_meth:
    name: seq_meth
    description: Sequencing machine used. Where possible the term should be taken
      from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)
    title: sequencing method
    examples:
    - value: 454 Genome Sequencer FLX [OBI:0000702]
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    slot_uri: MIXS:0000050
    alias: seq_meth
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
    structured_pattern:
      syntax: ^{text}|({termLabel} \[{termID}\])$
      interpolated: true
      partial_match: true
  lat_lon:
    name: lat_lon
    description: The geographical origin of the sample as defined by latitude and
      longitude. The values should be reported in decimal degrees, limited to 8 decimal
      points, and in WGS84 system
    title: geographic location (latitude and longitude)
    examples:
    - value: 50.586825 6.408977
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - geographic
    - location
    slot_uri: MIXS:0000009
    alias: lat_lon
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: string
    required: true
    pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$
    structured_pattern:
      syntax: ^{lat} {lon}$
      interpolated: true
      partial_match: true
  elev:
    name: elev
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit
    title: elevation
    examples:
    - value: 100 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - elevation
    slot_uri: MIXS:0000093
    alias: elev
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - HostAssociated
    - HydrocarbonResourcesCores
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - Water
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  env_broad_scale:
    name: env_broad_scale
    description: 'Report the major environmental system the sample or specimen came
      from. The system(s) identified should have a coarse spatial grain, to provide
      the general environmental context of where the sampling was done (e.g. in the
      desert or a rainforest). We recommend using subclasses of EnvO s biome class:  http://purl.obolibrary.org/obo/ENVO_00000428.
      EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: broad-scale environmental context
    examples:
    - value: rangeland biome [ENVO:01000247]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - context
    - environmental
    slot_uri: MIXS:0000012
    alias: env_broad_scale
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  tax_class:
    name: tax_class
    description: Method used for taxonomic classification, along with reference database
      used, classification rank, and thresholds used to classify new genomes
    title: taxonomic classification
    examples:
    - value: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification,
        default parameters)
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - classification
    - taxon
    slot_uri: MIXS:0000064
    alias: tax_class
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
  experimental_factor:
    name: experimental_factor
    annotations:
      Expected_value:
        tag: Expected_value
        value: text or EFO and/or OBI
    description: Variable aspects of an experiment design that can be used to describe
      an experiment, or set of experiments, in an increasingly detailed manner. This
      field accepts ontology terms from Experimental Factor Ontology (EFO) and/or
      Ontology for Biomedical Investigations (OBI)
    title: experimental factor
    examples:
    - value: time series design [EFO:0001779]
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - experimental
    - factor
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000008
    alias: experimental_factor
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    multivalued: true
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  associated_resource:
    name: associated_resource
    annotations:
      Expected_value:
        tag: Expected_value
        value: reference to resource
    description: A related resource that is referenced, cited, or otherwise associated
      to the sequence
    title: relevant electronic resources
    examples:
    - value: http://www.earthmicrobiome.org/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - resource
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000091
    alias: associated_resource
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    multivalued: true
  sop:
    name: sop
    annotations:
      Expected_value:
        tag: Expected_value
        value: reference to SOP
    description: Standard operating procedures used in assembly and/or annotation
      of genomes, metagenomes or environmental sequences
    title: relevant standard operating procedures
    examples:
    - value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - procedures
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000090
    alias: sop
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    multivalued: true
  humidity:
    name: humidity
    description: Amount of water vapour in the air, at the time of sampling
    title: humidity
    examples:
    - value: 30% relative humidity
    from_schema: https://w3id.org/mixs
    keywords:
    - humidity
    slot_uri: MIXS:0000100
    alias: humidity
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - Air
    - FoodFarmEnvironment
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  organism_count:
    name: organism_count
    annotations:
      Expected_value:
        tag: Expected_value
        value: organism name;measurement value;enumeration
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR
    from_schema: https://w3id.org/mixs
    keywords:
    - count
    - organism
    string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
    slot_uri: MIXS:0000103
    alias: organism_count
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  spikein_count:
    name: spikein_count
    annotations:
      Expected_value:
        tag: Expected_value
        value: organism name;measurement value;enumeration
      Preferred_unit:
        tag: Preferred_unit
        value: colony forming units per milliliter; colony forming units per gram
          of dry weight
    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: spike-in organism count
    examples:
    - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR
    from_schema: https://w3id.org/mixs
    keywords:
    - count
    - organism
    - spike
    string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
    slot_uri: MIXS:0001335
    alias: spikein_count
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
  samp_store_temp:
    name: samp_store_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature at which sample was stored, e.g. -80 degree Celsius
    title: sample storage temperature
    examples:
    - value: -80 degree Celsius
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - storage
    - temperature
    slot_uri: MIXS:0000110
    alias: samp_store_temp
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  solar_irradiance:
    name: solar_irradiance
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: kilowatts per square meter per day, ergs per square centimeter per
          second
    description: The amount of solar energy that arrives at a specific area of a surface
      during a specific time interval
    title: solar irradiance
    examples:
    - value: 1.36 kilowatts per square meter per day
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000112
    alias: solar_irradiance
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - Air
    - FoodFarmEnvironment
    range: string
    multivalued: 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
  ventilation_rate:
    name: ventilation_rate
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: cubic meter per minute, liters per second
    description: Ventilation rate of the system in the sampled premises
    title: ventilation rate
    examples:
    - value: 750 cubic meter per minute
    from_schema: https://w3id.org/mixs
    keywords:
    - rate
    slot_uri: MIXS:0000114
    alias: ventilation_rate
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Air
    - FoodFarmEnvironment
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_store_dur:
    name: samp_store_dur
    description: Duration for which the sample was stored. Indicate the duration for
      which the sample was stored written in ISO 8601 format
    title: sample storage duration
    examples:
    - value: P1Y6M
    from_schema: https://w3id.org/mixs
    keywords:
    - duration
    - period
    - sample
    - storage
    slot_uri: MIXS:0000116
    alias: samp_store_dur
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
    structured_pattern:
      syntax: ^{duration}$
      interpolated: true
      partial_match: true
  wind_speed:
    name: wind_speed
    description: speed of wind measured at the time of sampling
    title: wind speed
    examples:
    - value: 1.6 kilometers per hour
    from_schema: https://w3id.org/mixs
    keywords:
    - speed
    - wind
    slot_uri: MIXS:0000118
    alias: wind_speed
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Air
    - FoodFarmEnvironment
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  salinity:
    name: salinity
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: practical salinity unit, percentage
    description: The total concentration of all dissolved salts in a liquid or solid
      sample. While salinity can be measured by a complete chemical analysis, this
      method is difficult and time consuming. More often, it is instead derived from
      the conductivity measurement. This is known as practical salinity. These derivations
      compare the specific conductance of the sample to a salinity standard such as
      seawater
    title: salinity
    examples:
    - value: 25 practical salinity unit
    from_schema: https://w3id.org/mixs
    keywords:
    - salinity
    slot_uri: MIXS:0000183
    alias: salinity
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  previous_land_use:
    name: previous_land_use
    annotations:
      Expected_value:
        tag: Expected_value
        value: land use name;date
    description: Previous land use and dates
    title: history/previous land use
    examples:
    - value: fallow; 2018-05-11:T14:30Z
    from_schema: https://w3id.org/mixs
    keywords:
    - history
    - land
    - use
    string_serialization: '{text};{timestamp}'
    slot_uri: MIXS:0000315
    alias: previous_land_use
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
  crop_rotation:
    name: crop_rotation
    annotations:
      Expected_value:
        tag: Expected_value
        value: crop rotation status;schedule
    description: Whether or not crop is rotated, and if yes, rotation schedule
    title: history/crop rotation
    examples:
    - value: yes;R2/2017-01-01/2018-12-31/P6M
    from_schema: https://w3id.org/mixs
    keywords:
    - history
    string_serialization: '{boolean};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000318
    alias: crop_rotation
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
  soil_type_meth:
    name: soil_type_meth
    description: Reference or method used in determining soil series name or other
      lower-level classification
    title: soil type method
    examples:
    - value: https://www.lrh.usace.army.mil/Portals/38/docs/PR/BluestoneSFEIS/Appendix%20K-Soil%20Descriptions.pdf
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    - soil
    - type
    slot_uri: MIXS:0000334
    alias: soil_type_meth
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  tot_org_c_meth:
    name: tot_org_c_meth
    description: Reference or method used in determining total organic carbon
    title: total organic carbon method
    examples:
    - value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    - method
    - organic
    - total
    slot_uri: MIXS:0000337
    alias: tot_org_c_meth
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  tot_nitro_cont_meth:
    name: tot_nitro_cont_meth
    description: Reference or method used in determining the total nitrogen
    title: total nitrogen content method
    examples:
    - value: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00
    from_schema: https://w3id.org/mixs
    keywords:
    - content
    - method
    - nitrogen
    - total
    slot_uri: MIXS:0000338
    alias: tot_nitro_cont_meth
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  host_age:
    name: host_age
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: year, day, hour
    description: Age of host at the time of sampling; relevant scale depends on species
      and study, e.g. Could be seconds for amoebae or centuries for trees
    title: host age
    examples:
    - value: 10 days
    from_schema: https://w3id.org/mixs
    keywords:
    - age
    - host
    - host.
    slot_uri: MIXS:0000255
    alias: host_age
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_dry_mass:
    name: host_dry_mass
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: kilogram, gram
    description: Measurement of dry mass
    title: host dry mass
    examples:
    - value: 500 gram
    from_schema: https://w3id.org/mixs
    keywords:
    - dry
    - host
    - host.
    - mass
    slot_uri: MIXS:0000257
    alias: host_dry_mass
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_height:
    name: host_height
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: centimeter, millimeter, meter
    description: The height of subject
    title: host height
    examples:
    - value: 1 meter
    from_schema: https://w3id.org/mixs
    keywords:
    - height
    - host
    - host.
    slot_uri: MIXS:0000264
    alias: host_height
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_length:
    name: host_length
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: centimeter, millimeter, meter
    description: The length of subject
    title: host length
    examples:
    - value: 1 meter
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - length
    slot_uri: MIXS:0000256
    alias: host_length
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  host_tot_mass:
    name: host_tot_mass
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: kilogram, gram
    description: Total mass of the host at collection, the unit depends on host
    title: host total mass
    examples:
    - value: 2500 gram
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - mass
    - total
    slot_uri: MIXS:0000263
    alias: host_tot_mass
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  root_med_carbon:
    name: root_med_carbon
    annotations:
      Expected_value:
        tag: Expected_value
        value: carbon source name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter
    description: Source of organic carbon in the culture rooting medium; e.g. sucrose
    title: rooting medium carbon
    examples:
    - value: sucrose
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000577
    alias: root_med_carbon
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
  root_med_macronutr:
    name: root_med_macronutr
    annotations:
      Expected_value:
        tag: Expected_value
        value: macronutrient name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter
    description: Measurement of the culture rooting medium macronutrients (N,P, K,
      Ca, Mg, S); e.g. KH2PO4 (170 mg/L)
    title: rooting medium macronutrients
    examples:
    - value: KH2PO4;170  milligram per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - macronutrients
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000578
    alias: root_med_macronutr
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
  root_med_micronutr:
    name: root_med_micronutr
    annotations:
      Expected_value:
        tag: Expected_value
        value: micronutrient name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter
    description: Measurement of the culture rooting medium micronutrients (Fe, Mn,
      Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L)
    title: rooting medium micronutrients
    examples:
    - value: H3BO3;6.2  milligram per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - micronutrients
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000579
    alias: root_med_micronutr
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
  season_temp:
    name: season_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Mean seasonal temperature
    title: mean seasonal temperature
    examples:
    - value: 18 degree Celsius
    from_schema: https://w3id.org/mixs
    keywords:
    - mean
    - season
    - temperature
    slot_uri: MIXS:0000643
    alias: season_temp
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  season_precpt:
    name: season_precpt
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: millimeter
    description: The average of all seasonal precipitation values known, or an estimated
      equivalent value derived by such methods as regional indexes or Isohyetal maps
    title: mean seasonal precipitation
    examples:
    - value: 75 millimeters
    from_schema: https://w3id.org/mixs
    keywords:
    - mean
    - season
    slot_uri: MIXS:0000645
    alias: season_precpt
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  tot_org_carb:
    name: tot_org_carb
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: gram Carbon per kilogram sample material
    description: Total organic carbon content
    title: total organic carbon
    examples:
    - value: '0.02'
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    - organic
    - total
    slot_uri: MIXS:0000533
    alias: tot_org_carb
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - MicrobialMatBiofilm
    - Sediment
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  tot_nitro_content:
    name: tot_nitro_content
    description: Total nitrogen content of the sample
    title: total nitrogen content
    examples:
    - value: 35 milligrams Nitrogen per kilogram of soil
    from_schema: https://w3id.org/mixs
    keywords:
    - content
    - nitrogen
    - total
    slot_uri: MIXS:0000530
    alias: tot_nitro_content
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - MicrobialMatBiofilm
    - Sediment
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  conduc:
    name: conduc
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milliSiemens per centimeter
    description: Electrical conductivity of water
    title: conductivity
    examples:
    - value: 10 milliSiemens per centimeter
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000692
    alias: conduc
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  turbidity:
    name: turbidity
    description: Measure of the amount of cloudiness or haziness in water caused by
      individual particles
    title: turbidity
    examples:
    - value: 0.3 nephelometric turbidity units
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000191
    alias: turbidity
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  size_frac_low:
    name: size_frac_low
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micrometer
    description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.
      Materials smaller than the size threshold are excluded from the sample
    title: size-fraction lower threshold
    examples:
    - value: 0.2 micrometer
    from_schema: https://w3id.org/mixs
    keywords:
    - lower
    slot_uri: MIXS:0000735
    alias: size_frac_low
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  size_frac_up:
    name: size_frac_up
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micrometer
    description: Mesh or pore size of the device used to retain the sample. Materials
      larger than the size threshold are excluded from the sample.
    title: size-fraction upper threshold
    examples:
    - value: 20 micrometer
    from_schema: https://w3id.org/mixs
    keywords:
    - upper
    slot_uri: MIXS:0000736
    alias: size_frac_up
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  ventilation_type:
    name: ventilation_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: ventilation type name
    description: Ventilation system used in the sampled premises
    title: ventilation type
    examples:
    - value: Operable windows
    from_schema: https://w3id.org/mixs
    keywords:
    - type
    slot_uri: MIXS:0000756
    alias: ventilation_type
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Air
    - BuiltEnvironment
    - FoodFarmEnvironment
    range: string
    multivalued: true
  wind_direction:
    name: wind_direction
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degrees or cardinal direction
    description: Wind direction is the direction from which a wind originates
    title: wind direction
    examples:
    - value: 0 degrees; Northwest
    from_schema: https://w3id.org/mixs
    keywords:
    - direction
    - wind
    slot_uri: MIXS:0000757
    alias: wind_direction
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Air
    - FoodFarmEnvironment
    range: string
  genetic_mod:
    name: genetic_mod
    annotations:
      Expected_value:
        tag: Expected_value
        value: PMID, DOI, URL or text
    description: Genetic modifications of the genome of an organism, which may occur
      naturally by spontaneous mutation, or be introduced by some experimental means,
      e.g. specification of a transgene or the gene knocked-out or details of transient
      transfection
    title: genetic modification
    examples:
    - value: aox1A transgenic
    from_schema: https://w3id.org/mixs
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000859
    alias: genetic_mod
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - PlantAssociated
    range: string
  host_phenotype:
    name: host_phenotype
    annotations:
      Expected_value:
        tag: Expected_value
        value: PATO or HP
    description: Phenotype of human or other host. Use terms from the phenotypic quality
      ontology (pato) or the Human Phenotype Ontology (HP)
    title: host phenotype
    examples:
    - value: seed pod; green [PATO:0000320]
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000874
    alias: host_phenotype
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
  ph:
    name: ph
    description: Ph measurement of the sample, or liquid portion of sample, or aqueous
      phase of the fluid
    title: pH
    examples:
    - value: '7.2'
    from_schema: https://w3id.org/mixs
    keywords:
    - ph
    slot_uri: MIXS:0001001
    alias: ph
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Soil
    - WastewaterSludge
    - Water
    range: float
  ances_data:
    name: ances_data
    description: Information about either pedigree or other ancestral information
      description (e.g. parental variety in case of mutant or selection), e.g. A/3*B
      (meaning [(A x B) x B] x B)
    title: ancestral data
    examples:
    - value: A/3*B
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000247
    alias: ances_data
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    range: string
  biotic_regm:
    name: biotic_regm
    description: Information about treatment(s) involving use of biotic factors, such
      as bacteria, viruses or fungi
    title: biotic regimen
    examples:
    - value: sample inoculated with Rhizobium spp. Culture
    from_schema: https://w3id.org/mixs
    keywords:
    - regimen
    slot_uri: MIXS:0001038
    alias: biotic_regm
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
    required: true
    multivalued: true
  chem_administration:
    name: chem_administration
    annotations:
      Expected_value:
        tag: Expected_value
        value: CHEBI;timestamp
    description: List of chemical compounds administered to the host or site where
      sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
      include multiple compounds. For chemical entities of biological interest ontology
      (chebi) (v 163), http://purl.bioontology.org/ontology/chebi
    title: chemical administration
    examples:
    - value: agar [CHEBI:2509];2018-05-11T20:00Z
    from_schema: https://w3id.org/mixs
    keywords:
    - administration
    string_serialization: '{termLabel} [{termID}];{timestamp}'
    slot_uri: MIXS:0000751
    alias: chem_administration
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: true
    multivalued: true
  growth_habit:
    name: growth_habit
    description: Characteristic shape, appearance or growth form of a plant species
    title: growth habit
    examples:
    - value: spreading
    from_schema: https://w3id.org/mixs
    keywords:
    - growth
    slot_uri: MIXS:0001044
    alias: growth_habit
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    range: GrowthHabitEnum
  host_disease_stat:
    name: host_disease_stat
    annotations:
      Expected_value:
        tag: Expected_value
        value: disease name or Disease Ontology term
    description: List of diseases with which the host has been diagnosed; can include
      multiple diagnoses. The value of the field depends on host; for humans the terms
      should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
      non-human host diseases are free text
    title: host disease status
    examples:
    - value: downy mildew
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - disease
    - host
    - host.
    - status
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000031
    alias: host_disease_stat
    owner: MimagFoodFarmEnvironment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    range: string
    recommended: true
  host_genotype:
    name: host_genotype
    description: Observed genotype
    title: host genotype
    examples:
    - value: Ts
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    slot_uri: MIXS:0000365
    alias: host_genotype
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    - SymbiontAssociated
    range: string
  host_taxid:
    name: host_taxid
    annotations:
      Expected_value:
        tag: Expected_value
        value: NCBI taxon identifier
    description: NCBI taxon id of the host, e.g. 9606
    title: host taxid
    examples:
    - value: '4530'
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - taxon
    string_serialization: '{NCBI taxid}'
    slot_uri: MIXS:0000250
    alias: host_taxid
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    - SymbiontAssociated
    range: string
  mechanical_damage:
    name: mechanical_damage
    annotations:
      Expected_value:
        tag: Expected_value
        value: damage type;body site
    description: Information about any mechanical damage exerted on the plant; can
      include multiple damages and sites
    title: mechanical damage
    examples:
    - value: pruning;bark
    from_schema: https://w3id.org/mixs
    string_serialization: '{text};{text}'
    slot_uri: MIXS:0001052
    alias: mechanical_damage
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
    multivalued: true
  perturbation:
    name: perturbation
    annotations:
      Expected_value:
        tag: Expected_value
        value: perturbation type name;perturbation interval and duration
    description: Type of perturbation, e.g. chemical administration, physical disturbance,
      etc., coupled with perturbation regimen including how many times the perturbation
      was repeated, how long each perturbation lasted, and the start and end time
      of the entire perturbation period; can include multiple perturbation types
    title: perturbation
    examples:
    - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - perturbation
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000754
    alias: perturbation
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  root_cond:
    name: root_cond
    description: Relevant rooting conditions such as field plot size, sowing density,
      container dimensions, number of plants per container
    title: rooting conditions
    examples:
    - value: http://himedialabs.com/TD/PT158.pdf
    from_schema: https://w3id.org/mixs
    keywords:
    - condition
    slot_uri: MIXS:0001061
    alias: root_cond
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: true
  root_med_ph:
    name: root_med_ph
    description: pH measurement of the culture rooting medium; e.g. 5.5
    title: rooting medium pH
    examples:
    - value: '7.5'
    from_schema: https://w3id.org/mixs
    keywords:
    - ph
    slot_uri: MIXS:0001062
    alias: root_med_ph
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - PlantAssociated
    range: float
  tillage:
    name: tillage
    description: Note method(s) used for tilling
    title: history/tillage
    examples:
    - value: chisel
    from_schema: https://w3id.org/mixs
    keywords:
    - history
    slot_uri: MIXS:0001081
    alias: tillage
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: TillageEnum
    multivalued: true
  ph_meth:
    name: ph_meth
    description: Reference or method used in determining pH
    title: pH method
    examples:
    - value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    - ph
    slot_uri: MIXS:0001106
    alias: ph_meth
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  growth_medium:
    name: growth_medium
    description: A liquid or gel containing nutrients, salts, and other factors formulated
      to support the growth of microorganisms, cells, or plants (National Cancer Institute
      Thesaurus).  The name of the medium used to grow the microorganism
    title: growth medium
    examples:
    - value: LB broth
    from_schema: https://w3id.org/mixs
    keywords:
    - growth
    slot_uri: MIXS:0001108
    alias: growth_medium
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    range: string
  season:
    name: season
    annotations:
      Expected_value:
        tag: Expected_value
        value: autumn [NCIT:C94733], spring [NCIT:C94731], summer [NCIT:C94732], winter
          [NCIT:C94730]
    description: The season when sampling occurred. Any of the four periods into which
      the year is divided by the equinoxes and solstices. This field accepts terms
      listed under season (http://purl.obolibrary.org/obo/NCIT_C94729)
    title: season
    comments:
    - autumn [NCIT:C94733] does not match ^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$
    - would require ^\\S+.*\\S+ \\[[a-zA-Z]{2,}:[a-zA-Z0-9]\\]$
    examples:
    - value: autumn [NCIT:C94733]
    from_schema: https://w3id.org/mixs
    keywords:
    - season
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000829
    alias: season
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - BuiltEnvironment
    - FoodFarmEnvironment
    range: string
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:[a-zA-Z0-9]+\]$
  food_product_type:
    name: food_product_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:00001002 or FOODON:03309997
    description: A food product type is a class of food products that is differentiated
      by its food composition (e.g., single- or multi-ingredient), processing and/or
      consumption characteristics. This does not include brand name products but it
      may include generic food dish categories. This field accepts terms under food
      product type (http://purl.obolibrary.org/obo/FOODON:03400361). For terms related
      to food product for an animal, consult food product for animal (http://purl.obolibrary.org/obo/FOODON_03309997).
      If the proper descriptor is not listed please use text to describe the food
      type. Multiple terms can be separated by one or more pipes
    title: food product type
    examples:
    - value: shrimp (peeled, deep-frozen) [FOODON:03317171]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - product
    - type
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001184
    alias: food_product_type
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
  samp_type:
    name: samp_type
    description: The type of material from which the sample was obtained. For the
      Hydrocarbon package, samples include types like core, rock trimmings, drill
      cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid,
      produced water, injected water, swabs, etc. For the Food Package, samples are
      usually categorized as food, body products or tissues, or environmental material.
      This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246)
    title: sample type
    examples:
    - value: built environment sample [GENEPIO:0001248]
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - type
    slot_uri: MIXS:0000998
    alias: samp_type
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    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
  farm_water_source:
    name: farm_water_source
    description: Source of water used on the farm for irrigation of crops or watering
      of livestock
    title: farm watering water source
    examples:
    - value: well
      description: was water well (ENVO:01000002)
    from_schema: https://w3id.org/mixs
    keywords:
    - farm
    - source
    - water
    slot_uri: MIXS:0001110
    alias: farm_water_source
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: FarmWaterSourceEnum
    recommended: true
  plant_water_method:
    name: plant_water_method
    description: Description of the equipment or method used to distribute water to
      crops. This field accepts termed listed under irrigation process (http://purl.obolibrary.org/obo/AGRO_00000006).
      Multiple terms can be separated by pipes
    title: plant water delivery method
    examples:
    - value: drip irrigation process [AGRO:00000056]
    from_schema: https://w3id.org/mixs
    keywords:
    - delivery
    - method
    - plant
    - water
    slot_uri: MIXS:0001111
    alias: plant_water_method
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: string
    recommended: 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
  air_PM_concen:
    name: air_PM_concen
    description: Concentration of substances that remain suspended in the air, and
      comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can
      report multiple PM's by entering numeric values preceded by name of PM
    title: air particulate matter concentration
    examples:
    - value: PM2.5;10 microgram per cubic meter
    from_schema: https://w3id.org/mixs
    keywords:
    - air
    - concentration
    - particle
    - particulate
    slot_uri: MIXS:0000108
    alias: air_PM_concen
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Air
    - FoodFarmEnvironment
    range: string
    multivalued: true
    structured_pattern:
      syntax: ^{particulate_matter_name};{float} {unit}$
      interpolated: true
      partial_match: true
  animal_feed_equip:
    name: animal_feed_equip
    annotations:
      Expected_value:
        tag: Expected_value
        value: EOL:0001757
    description: Description of the feeding equipment used for livestock. This field
      accepts terms listed under feed delivery (http://opendata.inra.fr/EOL/EOL_0001757).
      Multiple terms can be separated by pipes
    title: animal feeding equipment
    examples:
    - value: self feeding [EOL:0001645]| straight feed trough [EOL:0001661]
    from_schema: https://w3id.org/mixs
    keywords:
    - animal
    - equipment
    slot_uri: MIXS:0001113
    alias: animal_feed_equip
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    range: string
    multivalued: true
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  animal_intrusion:
    name: animal_intrusion
    description: Identification of animals intruding on the sample or sample site
      including invertebrates (such as pests or pollinators) and vertebrates (such
      as wildlife or domesticated animals). This field accepts terms under organism
      (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification
      numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms
      can be separated by pipes
    title: animal intrusion near sample source
    examples:
    - value: Thripidae [NCBITaxon:45053]
    from_schema: https://w3id.org/mixs
    keywords:
    - animal
    - sample
    - source
    slot_uri: MIXS:0001114
    alias: animal_intrusion
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    range: string
    multivalued: true
    pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$
    structured_pattern:
      syntax: ^({termLabel} \[{termID}\])|{integer}$
      interpolated: true
      partial_match: true
  anim_water_method:
    name: anim_water_method
    description: Description of the equipment or method used to distribute water to
      livestock. This field accepts termed listed under water delivery equipment (http://opendata.inra.fr/EOL/EOL_0001653).
      Multiple terms can be separated by pipes
    title: animal water delivery method
    examples:
    - value: water trough [EOL:0001618]
    from_schema: https://w3id.org/mixs
    keywords:
    - animal
    - delivery
    - method
    - water
    slot_uri: MIXS:0001115
    alias: anim_water_method
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: string
    multivalued: 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
  crop_yield:
    name: crop_yield
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: kilogram per metre square
    description: Amount of crop produced per unit or area of land
    title: crop yield
    examples:
    - value: 570 kilogram per metre square
    from_schema: https://w3id.org/mixs
    keywords:
    - crop
    slot_uri: MIXS:0001116
    alias: crop_yield
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  cult_result:
    name: cult_result
    description: Any result of a bacterial culture experiment reported as a binary
      assessment such as positive/negative, active/inactive
    title: culture result
    examples:
    - value: positive
    from_schema: https://w3id.org/mixs
    keywords:
    - culture
    slot_uri: MIXS:0001117
    alias: cult_result
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: CultResultEnum
  cult_result_org:
    name: cult_result_org
    description: Taxonomic information about the cultured organism(s)
    title: culture result organism
    examples:
    - value: Listeria monocytogenes [NCIT:C86502]
    from_schema: https://w3id.org/mixs
    keywords:
    - culture
    - organism
    slot_uri: MIXS:0001118
    alias: cult_result_org
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
    pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$
    structured_pattern:
      syntax: ^({termLabel} \[{termID}\])|{integer}$
      interpolated: true
      partial_match: true
  cult_target:
    name: cult_target
    annotations:
      Expected_value:
        tag: Expected_value
        value: NCIT:C14250 or NCBI taxid or culture independent
    description: The target microbial analyte in terms of investigation scope. This
      field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250).
      This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy
    title: culture target microbial analyte
    examples:
    - value: Listeria monocytogenes [NCIT:C86502]
    from_schema: https://w3id.org/mixs
    keywords:
    - culture
    - microbial
    - target
    string_serialization: '{termLabel} [{termID}]|{integer}'
    slot_uri: MIXS:0001119
    alias: cult_target
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  plant_part_maturity:
    name: plant_part_maturity
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03530050
    description: A description of the stage of development of a plant or plant part
      based on maturity or ripeness. This field accepts terms listed under degree
      of plant maturity (http://purl.obolibrary.org/obo/FOODON_03530050)
    title: degree of plant part maturity
    examples:
    - value: ripe or mature [FOODON:03530052]
    from_schema: https://w3id.org/mixs
    keywords:
    - degree
    - plant
    string_serialization: '{term label}{term ID}'
    slot_uri: MIXS:0001120
    alias: plant_part_maturity
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    range: string
  adjacent_environment:
    name: adjacent_environment
    annotations:
      Expected_value:
        tag: Expected_value
        value: ENVO_01001110 or ENVO_00000070
    description: Description of the environmental system or features that are adjacent
      to the sampling site. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110)
      and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple
      terms can be separated by pipes
    title: environment adjacent to site
    examples:
    - value: estuarine biome [ENVO:01000020]
    from_schema: https://w3id.org/mixs
    keywords:
    - adjacent
    - environment
    - site
    string_serialization: '{termLabel}{[termID]}'
    slot_uri: MIXS:0001121
    alias: adjacent_environment
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: string
    multivalued: true
  water_source_adjac:
    name: water_source_adjac
    annotations:
      Expected_value:
        tag: Expected_value
        value: ENVO_01001110 or ENVO_00000070
    description: Description of the environmental features that are adjacent to the
      farm water source. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110)
      and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple
      terms can be separated by pipes
    title: environmental feature adjacent water source
    examples:
    - value: feedlot [ENVO:01000627]
    from_schema: https://w3id.org/mixs
    keywords:
    - adjacent
    - environmental
    - feature
    - source
    - water
    slot_uri: MIXS:0001122
    alias: water_source_adjac
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    range: string
    multivalued: true
  farm_equip_shared:
    name: farm_equip_shared
    description: List of planting, growing or harvesting equipment shared with other
      farms. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416).
      Multiple terms can be separated by pipes
    title: equipment shared with other farms
    examples:
    - value: combine harvester [AGRO:00000473]
    from_schema: https://w3id.org/mixs
    keywords:
    - equipment
    - farm
    slot_uri: MIXS:0001123
    alias: farm_equip_shared
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: string
    multivalued: 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
  farm_equip_san:
    name: farm_equip_san
    annotations:
      Expected_value:
        tag: Expected_value
        value: text or commercial name of sanitizer or class of sanitizer or active
          ingredient in sanitizer
      Preferred_unit:
        tag: Preferred_unit
        value: parts per million
    description: Method used to sanitize growing and harvesting equipment. This can
      including type and concentration of sanitizing solution.  Multiple terms can
      be separated by one or more pipes
    title: farm equipment sanitization
    examples:
    - value: hot water pressure wash, hypochlorite solution, 50 parts per million
    from_schema: https://w3id.org/mixs
    keywords:
    - equipment
    - farm
    string_serialization: '{text} {float} {unit}'
    slot_uri: MIXS:0001124
    alias: farm_equip_san
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: string
    multivalued: true
  farm_equip_san_freq:
    name: farm_equip_san_freq
    description: The number of times farm equipment is cleaned. Frequency of cleaning
      might be on a Daily basis, Weekly, Monthly, Quarterly or Annually
    title: farm equipment sanitization frequency
    examples:
    - value: Biweekly
    from_schema: https://w3id.org/mixs
    keywords:
    - equipment
    - farm
    - frequency
    slot_uri: MIXS:0001125
    alias: farm_equip_san_freq
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    range: string
  farm_equip:
    name: farm_equip
    description: List of equipment used for planting, fertilization, harvesting, irrigation,
      land levelling, residue management, weeding or transplanting during the growing
      season.  This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416).
      Multiple terms can be separated by pipes
    title: farm equipment used
    examples:
    - value: combine harvester [AGRO:00000473]
    from_schema: https://w3id.org/mixs
    keywords:
    - equipment
    - farm
    - use
    slot_uri: MIXS:0001126
    alias: farm_equip
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: string
    multivalued: 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
  fertilizer_admin:
    name: fertilizer_admin
    description: Type of fertilizer or amendment added to the soil or water for the
      purpose of improving substrate health and quality for plant growth. This field
      accepts terms listed under agronomic fertilizer (http://purl.obolibrary.org/obo/AGRO_00002062).
      Multiple terms may apply and can be separated by pipes, listing in reverse chronological
      order
    title: fertilizer administration
    examples:
    - value: fish emulsion [AGRO:00000082]
    from_schema: https://w3id.org/mixs
    keywords:
    - administration
    slot_uri: MIXS:0001127
    alias: fertilizer_admin
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: string
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  fertilizer_date:
    name: fertilizer_date
    description: Date of administration of soil amendment or fertilizer. Multiple
      terms may apply and can be separated by pipes, listing in reverse chronological
      order
    title: fertilizer administration date
    examples:
    - value: '2018-05-11T10:00:00+01:00'
    from_schema: https://w3id.org/mixs
    keywords:
    - administration
    - date
    slot_uri: MIXS:0001128
    alias: fertilizer_date
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    range: datetime
  animal_group_size:
    name: animal_group_size
    description: The number of food animals of the same species that are maintained
      together as a unit, i.e. a herd or flock
    title: food animal group size
    examples:
    - value: '80'
    from_schema: https://w3id.org/mixs
    keywords:
    - animal
    - food
    - size
    slot_uri: MIXS:0001129
    alias: animal_group_size
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    range: integer
  animal_diet:
    name: animal_diet
    annotations:
      Expected_value:
        tag: Expected_value
        value: text or FOODON_03309997
    description: If the isolate is from a food animal, the type of diet eaten by the
      food animal.  Please list the main food staple and the setting, if appropriate.  For
      a list of acceptable animal feed terms or categories, please see http://www.feedipedia.org.  Multiple
      terms may apply and can be separated by pipes |Food product for animal covers
      foods intended for consumption by domesticated animals. Consult http://purl.obolibrary.org/obo/FOODON_03309997.
      If the proper descriptor is not listed please use text to describe the food
      type. Multiple terms can be separated by one or more pipes. If the proper descriptor
      is not listed please use text to describe the food product type
    title: food animal source diet
    examples:
    - value: Hay [FOODON:03301763]
    from_schema: https://w3id.org/mixs
    keywords:
    - animal
    - diet
    - food
    - source
    slot_uri: MIXS:0001130
    alias: animal_diet
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    range: string
    multivalued: true
  food_contact_surf:
    name: food_contact_surf
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03500010
    description: The specific container or coating materials in direct contact with
      the food. Multiple values can be assigned.  This field accepts terms listed
      under food contact surface (http://purl.obolibrary.org/obo/FOODON_03500010)
    title: food contact surface
    examples:
    - value: cellulose acetate [FOODON:03500034]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - surface
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001131
    alias: food_contact_surf
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  food_contain_wrap:
    name: food_contain_wrap
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03490100
    description: Type of container or wrapping defined by the main container material,
      the container form, and the material of the liner lids or ends. Also type of
      container or wrapping by form; prefer description by material first, then by
      form. This field accepts terms listed under food container or wrapping (http://purl.obolibrary.org/obo/FOODON_03490100)
    title: food container or wrapping
    examples:
    - value: Plastic shrink-pack [FOODON:03490137]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001132
    alias: food_contain_wrap
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  food_harvest_proc:
    name: food_harvest_proc
    description: A harvesting process is a process which takes in some food material
      from an individual or community of plant or animal organisms in a given context
      and time, and outputs a precursor or consumable food product. This may include
      a part of an organism or the whole, and may involve killing the organism
    title: Food harvesting process
    examples:
    - value: hand-picked
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - process
    slot_uri: MIXS:0001133
    alias: food_harvest_proc
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: string
    multivalued: true
  food_pack_medium:
    name: food_pack_medium
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03480020
    description: The medium in which the food is packed for preservation and handling
      or the medium surrounding homemade foods, e.g., peaches cooked in sugar syrup.
      The packing medium may provide a controlled environment for the food. It may
      also serve to improve palatability and consumer appeal.  This includes edible
      packing media (e.g. fruit juice), gas other than air (e.g. carbon dioxide),
      vacuum packed, or packed with aerosol propellant. This field accepts terms under
      food packing medium (http://purl.obolibrary.org/obo/FOODON_03480020). Multiple
      terms may apply and can be separated by pipes
    title: food packing medium
    examples:
    - value: vacuum-packed [FOODON:03480027]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001134
    alias: food_pack_medium
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  food_preserv_proc:
    name: food_preserv_proc
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03470107
    description: The methods contributing to the prevention or retardation of microbial,
      enzymatic or oxidative spoilage and thus to the extension of shelf life. This
      field accepts terms listed under food preservation process (http://purl.obolibrary.org/obo/FOODON_03470107)
    title: food preservation process
    examples:
    - value: food slow freezing [FOODON:03470128]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - process
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001135
    alias: food_preserv_proc
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  food_prod_char:
    name: food_prod_char
    description: Descriptors of the food production system such as wild caught, free-range,
      organic, free-range, industrial, dairy, beef
    title: food production characteristics
    examples:
    - value: wild caught
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - production
    slot_uri: MIXS:0001136
    alias: food_prod_char
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    range: string
    multivalued: true
  prod_label_claims:
    name: prod_label_claims
    description: Labeling claims containing descriptors such as wild caught, free-range,
      organic, free-range, industrial, hormone-free, antibiotic free, cage free. Can
      include more than one term, separated by ";"
    title: production labeling claims
    examples:
    - value: free range
    from_schema: https://w3id.org/mixs
    keywords:
    - production
    slot_uri: MIXS:prod_label_claims
    alias: prod_label_claims
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    range: string
    multivalued: true
  food_trav_mode:
    name: food_trav_mode
    description: A descriptor for the method of movement of food commodity along the
      food distribution system.  This field accepts terms listed under travel mode
      (http://purl.obolibrary.org/obo/GENEPIO_0001064). If the proper descrptor is
      not listed please use text to describe the mode of travel. Multiple terms can
      be separated by one or more pipes
    title: food shipping transportation method
    examples:
    - value: train travel [GENEPIO:0001060]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - method
    - transport
    slot_uri: MIXS:0001137
    alias: food_trav_mode
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: 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
  food_trav_vehic:
    name: food_trav_vehic
    annotations:
      Expected_value:
        tag: Expected_value
        value: ENVO:01000604
    description: A descriptor for the mobile machine which is used to transport food
      commodities along the food distribution system.  This field accepts terms listed
      under vehicle (http://purl.obolibrary.org/obo/ENVO_01000604). If the proper
      descrptor is not listed please use text to describe the mode of travel. Multiple
      terms can be separated by one or more pipes
    title: food shipping transportation vehicle
    examples:
    - value: aircraft [ENVO:01001488]|car [ENVO:01000605]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - transport
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001138
    alias: food_trav_vehic
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  food_source:
    name: food_source
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON term
    description: Type of plant or animal from which the food product or its major
      ingredient is derived or a chemical food source [FDA CFSAN 1995]
    title: food source
    examples:
    - value: giant tiger prawn [FOODON:03412612]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - source
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0001139
    alias: food_source
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  food_treat_proc:
    name: food_treat_proc
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03460111
    description: Used to specifically characterize a food product based on the treatment
      or processes applied to the product or any indexed ingredient. The processes
      include adding, substituting or removing components or modifying the food or
      component, e.g., through fermentation. Multiple values can be assigned. This
      fields accepts terms listed under food treatment process (http://purl.obolibrary.org/obo/FOODON_03460111)
    title: food treatment process
    examples:
    - value: gluten removal process [FOODON:03460750]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - process
    - treatment
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001140
    alias: food_treat_proc
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  extr_weather_event:
    name: extr_weather_event
    description: Unusual weather events that may have affected microbial populations.
      Multiple terms can be separated by pipes, listed in reverse chronological order
    title: extreme weather event
    examples:
    - value: hail
    from_schema: https://w3id.org/mixs
    keywords:
    - event
    - extreme
    - weather
    slot_uri: MIXS:0001141
    alias: extr_weather_event
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    range: ExtrWeatherEventEnum
    multivalued: true
  date_extr_weath:
    name: date_extr_weath
    description: Date of unusual weather events that may have affected microbial populations.
      Multiple terms can be separated by pipes, listed in reverse chronological order
    title: extreme weather date
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    from_schema: https://w3id.org/mixs
    keywords:
    - date
    - extreme
    - weather
    slot_uri: MIXS:0001142
    alias: date_extr_weath
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    range: datetime
    multivalued: true
  host_subspecf_genlin:
    name: host_subspecf_genlin
    annotations:
      Expected_value:
        tag: Expected_value
        value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,
          e.g. serovar, biotype, ecotype, variety, cultivar
    description: Information about the genetic distinctness of the host organism below
      the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,
      or any relevant genetic typing schemes like Group I plasmid. Subspecies should
      not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage
      name and the lineage rank separated by a colon, e.g., biovar:abc123
    title: host subspecific genetic lineage
    examples:
    - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'
    from_schema: https://w3id.org/mixs
    keywords:
    - host
    - host.
    - lineage
    string_serialization: '{rank name}:{text}'
    slot_uri: MIXS:0001318
    alias: host_subspecf_genlin
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - PlantAssociated
    range: string
    multivalued: true
  intended_consumer:
    name: intended_consumer
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON_03510136 or NCBI taxid
    description: Food consumer type, human or animal, for which the food product is
      produced and marketed. This field accepts terms listed under food consumer group
      (http://purl.obolibrary.org/obo/FOODON_03510136) or NCBI taxid
    title: intended consumer
    examples:
    - value: 9606 o rsenior as food consumer [FOODON:03510254]
    from_schema: https://w3id.org/mixs
    keywords:
    - consumer
    string_serialization: '{integer}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001144
    alias: intended_consumer
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  library_prep_kit:
    name: library_prep_kit
    annotations:
      Expected_value:
        tag: Expected_value
        value: name of library preparation kit
    description: Packaged kits (containing adapters, indexes, enzymes, buffers etc.),
      tailored for specific sequencing workflows, which allow the simplified preparation
      of sequencing-ready libraries for small genomes, amplicons, and plasmids
    title: library preparation kit
    examples:
    - value: Illumina DNA Prep
    from_schema: https://w3id.org/mixs
    keywords:
    - kit
    - library
    - preparation
    slot_uri: MIXS:0001145
    alias: library_prep_kit
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  air_flow_impede:
    name: air_flow_impede
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration;obstruction type; distance from sampling device
    description: Presence of objects in the area that would influence or impede air
      flow through the air filter
    title: local air flow impediments
    examples:
    - value: obstructed;hay bales; 2 m
    from_schema: https://w3id.org/mixs
    keywords:
    - air
    string_serialization: '[obstructed|unobstructed]; {text}; {measurement value}'
    slot_uri: MIXS:0001146
    alias: air_flow_impede
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    range: string
    multivalued: true
  lot_number:
    name: lot_number
    annotations:
      Expected_value:
        tag: Expected_value
        value: lot number, item
    description: 'A distinctive alpha-numeric identification code assigned by the
      manufacturer or distributor to a specific quantity of manufactured material
      or product within a batch. Synonym: Batch Number.  The submitter should provide
      lot number of the item followed by the item name for which the lot number was
      provided'
    title: lot number
    examples:
    - value: 1239ABC01A, split Cornish hens
    from_schema: https://w3id.org/mixs
    keywords:
    - number
    string_serialization: '{integer}, {text}'
    slot_uri: MIXS:0001147
    alias: lot_number
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  season_humidity:
    name: season_humidity
    description: Average humidity of the region throughout the growing season
    title: mean seasonal humidity
    comments:
    - percent or float?
    examples:
    - value: '0.25'
    from_schema: https://w3id.org/mixs
    keywords:
    - humidity
    - mean
    - season
    slot_uri: MIXS:0001148
    alias: season_humidity
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: float
    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
  part_plant_animal:
    name: part_plant_animal
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03420116
    description: The anatomical part of the organism being involved in food production
      or consumption; e.g., a carrot is the root of the plant (root vegetable). This
      field accepts terms listed under part of plant or animal (http://purl.obolibrary.org/obo/FOODON_03420116)
    title: part of plant or animal
    examples:
    - value: chuck [FOODON:03530021]
    from_schema: https://w3id.org/mixs
    keywords:
    - animal
    - plant
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001149
    alias: part_plant_animal
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  plant_growth_med:
    name: plant_growth_med
    annotations:
      Expected_value:
        tag: Expected_value
        value: EO or enumeration
    description: Specification of the media for growing the plants or tissue cultured
      samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in
      vitro liquid culture medium. Recommended value is a specific value from EO:plant
      growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147)
      or other controlled vocabulary
    title: plant growth medium
    examples:
    - value: soil
    from_schema: https://w3id.org/mixs
    keywords:
    - growth
    - plant
    string_serialization: '{termLabel} [{termID}] or [husk|other artificial liquid
      medium|other artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water]'
    slot_uri: MIXS:0001057
    alias: plant_growth_med
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - PlantAssociated
    range: string
  plant_reprod_crop:
    name: plant_reprod_crop
    description: Plant reproductive part used in the field during planting to start
      the crop
    title: plant reproductive part
    examples:
    - value: seedling
    from_schema: https://w3id.org/mixs
    keywords:
    - plant
    slot_uri: MIXS:0001150
    alias: plant_reprod_crop
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    range: PlantReprodCropEnum
    multivalued: true
  samp_purpose:
    name: samp_purpose
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration or {text}
    description: The reason that the sample was collected
    title: purpose of sampling
    examples:
    - value: field trial
    from_schema: https://w3id.org/mixs
    keywords:
    - purpose
    string_serialization: '[active surveillance in response to an outbreak|active
      surveillance not initiated by an outbreak|clinical trial|cluster investigation|environmental
      assessment|farm sample|field trial|for cause|industry internal investigation|market
      sample|passive surveillance|population based studies|research|research and development]
      or {text}'
    slot_uri: MIXS:0001151
    alias: samp_purpose
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  repository_name:
    name: repository_name
    annotations:
      Expected_value:
        tag: Expected_value
        value: Institution
    description: The name of the institution where the sample or DNA extract is held
      or "sample not available" if the sample was used in its entirety for analysis
      or otherwise not retained
    title: repository name
    examples:
    - value: FDA CFSAN Microbiology Laboratories
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0001152
    alias: repository_name
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  samp_pooling:
    name: samp_pooling
    description: Physical combination of several instances of like material, e.g.
      RNA extracted from samples or dishes of cell cultures into one big aliquot of
      cells. Please provide a short description of the samples that were pooled
    title: sample pooling
    examples:
    - value: 5uL of extracted genomic DNA from 5 leaves were pooled
    from_schema: https://w3id.org/mixs
    keywords:
    - pooling
    - sample
    slot_uri: MIXS:0001153
    alias: samp_pooling
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  samp_source_mat_cat:
    name: samp_source_mat_cat
    annotations:
      Expected_value:
        tag: Expected_value
        value: GENEPIO:0001237
    description: This is the scientific role or category that the subject organism
      or material has with respect to an investigation.  This field accepts terms
      listed under specimen source material category (http://purl.obolibrary.org/obo/GENEPIO_0001237
      or http://purl.obolibrary.org/obo/OBI_0100051)
    title: sample source material category
    examples:
    - value: environmental (swab or sampling) [GENEPIO:0001732]
    from_schema: https://w3id.org/mixs
    keywords:
    - material
    - sample
    - source
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0001154
    alias: samp_source_mat_cat
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  sequencing_kit:
    name: sequencing_kit
    annotations:
      Expected_value:
        tag: Expected_value
        value: name of sequencing kit used
    description: Pre-filled, ready-to-use reagent cartridges. Used to produce improved
      chemistry, cluster density and read length as well as improve quality (Q) scores.
      Reagent components are encoded to interact with the sequencing system to validate
      compatibility with user-defined applications. Indicate name of the sequencing
      kit
    title: sequencing kit
    examples:
    - value: NextSeq 500/550 High Output Kit v2.5 (75 Cycles)
    from_schema: https://w3id.org/mixs
    keywords:
    - kit
    slot_uri: MIXS:0001155
    alias: sequencing_kit
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  sequencing_location:
    name: sequencing_location
    description: The location the sequencing run was performed. Indicate the name
      of the lab or core facility where samples were sequenced
    title: sequencing location
    examples:
    - value: University of Maryland Genomics Resource Center
    from_schema: https://w3id.org/mixs
    keywords:
    - location
    slot_uri: MIXS:0001156
    alias: sequencing_location
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  serovar_or_serotype:
    name: serovar_or_serotype
    description: A characterization of a cell or microorganism based on the antigenic
      properties of the molecules on its surface. Indicate the name of a serovar or
      serotype of interest. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250).
      This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy
    title: serovar or serotype
    examples:
    - value: Escherichia coli strain O157:H7 [NCIT:C86883]
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0001157
    alias: serovar_or_serotype
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    multivalued: true
    pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$
    structured_pattern:
      syntax: ^({termLabel} \[{termID}\])|{integer}$
      interpolated: true
      partial_match: true
  soil_conductivity:
    name: soil_conductivity
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milliSiemens per centimeter
    description: Conductivity of soil at time of sampling.
    title: soil conductivity
    examples:
    - value: 10 milliSiemens per centimeter
    from_schema: https://w3id.org/mixs
    keywords:
    - soil
    slot_uri: MIXS:0001158
    alias: soil_conductivity
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  soil_cover:
    name: soil_cover
    annotations:
      Expected_value:
        tag: Expected_value
        value: subclass of 'environmental material', http://purl.obolibrary.org/obo/ENVO_00010483
    description: Material covering the sampled soil. This field accepts terms under
      ENVO:00010483, environmental material
    title: soil cover
    examples:
    - value: bare soil [ENVO01001616]
    from_schema: https://w3id.org/mixs
    keywords:
    - soil
    string_serialization: bare soil [ENVO:01001616]
    slot_uri: MIXS:0001159
    alias: soil_cover
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: string
  soil_pH:
    name: soil_pH
    description: The pH of soil at time of sampling.
    title: soil pH
    examples:
    - value: '7.2'
    from_schema: https://w3id.org/mixs
    keywords:
    - ph
    - soil
    slot_uri: MIXS:0001160
    alias: soil_pH
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: float
  rel_location:
    name: rel_location
    description: Location of sampled soil to other parts of the farm e.g. under crop
      plant, near irrigation ditch, from the dirt road
    title: relative location of sample
    examples:
    - value: furrow
    from_schema: https://w3id.org/mixs
    keywords:
    - location
    - relative
    - sample
    slot_uri: MIXS:0001161
    alias: rel_location
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: string
  soil_porosity:
    name: soil_porosity
    annotations:
      Expected_value:
        tag: Expected_value
        value: percent porosity
      Preferred_unit:
        tag: Preferred_unit
        value: percentage
    description: Porosity of soil or deposited sediment is volume of voids divided
      by the total volume of sample
    title: soil sediment porosity
    examples:
    - value: '0.2'
    from_schema: https://w3id.org/mixs
    keywords:
    - porosity
    - sediment
    - soil
    string_serialization: '{percentage}'
    slot_uri: MIXS:0001162
    alias: soil_porosity
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    range: string
  soil_temp:
    name: soil_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature of soil at the time of sampling
    title: soil temperature
    examples:
    - value: 25 degrees Celsius
    from_schema: https://w3id.org/mixs
    keywords:
    - soil
    - temperature
    slot_uri: MIXS:0001163
    alias: soil_temp
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  soil_texture_class:
    name: soil_texture_class
    description: One of the 12 soil texture classes use to describe soil texture based
      on the relative proportion of different grain sizes  of mineral particles [sand
      (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um)] in a soil
    title: soil texture classification
    examples:
    - value: silty clay loam
    from_schema: https://w3id.org/mixs
    keywords:
    - classification
    - soil
    - texture
    slot_uri: MIXS:0001164
    alias: soil_texture_class
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    range: SoilTextureClassEnum
  soil_texture_meth:
    name: soil_texture_meth
    description: Reference or method used in determining soil texture
    title: soil texture method
    examples:
    - value: https://uwlab.soils.wisc.edu/wp-content/uploads/sites/17/2015/09/particle_size.pdf
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    - soil
    - texture
    slot_uri: MIXS:0000336
    alias: soil_texture_meth
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  soil_type:
    name: soil_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: ENVO:00001998
    description: Description of the soil type or classification. This field accepts
      terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998).  Multiple terms
      can be separated by pipes
    title: soil type
    examples:
    - value: plinthosol [ENVO:00002250]
    from_schema: https://w3id.org/mixs
    keywords:
    - soil
    - type
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000332
    alias: soil_type
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
  spikein_org:
    name: spikein_org
    description: Taxonomic information about the spike-in organism(s). This field
      accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This
      field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy.
      Multiple terms can be separated by pipes
    title: spike in organism
    examples:
    - value: Listeria monocytogenes [NCIT:C86502]|28901
    from_schema: https://w3id.org/mixs
    keywords:
    - organism
    - spike
    slot_uri: MIXS:0001167
    alias: spikein_org
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    multivalued: true
    pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$
    structured_pattern:
      syntax: ^({termLabel} \[{termID}\])|{integer}$
      interpolated: true
      partial_match: true
  spikein_serovar:
    name: spikein_serovar
    annotations:
      Expected_value:
        tag: Expected_value
        value: NCIT:C14250 or antigenic formula or serovar name
    description: Taxonomic information about the spike-in organism(s) at the serovar
      or serotype level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250).
      This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy.
      Multiple terms can be separated by pipes
    title: spike-in bacterial serovar or serotype
    examples:
    - value: Escherichia coli strain O157:H7 [NCIT:C86883]|83334
    from_schema: https://w3id.org/mixs
    keywords:
    - spike
    string_serialization: '{termLabel} [{termID}]|{integer}'
    slot_uri: MIXS:0001168
    alias: spikein_serovar
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    multivalued: true
  spikein_growth_med:
    name: spikein_growth_med
    description: A liquid or gel containing nutrients, salts, and other factors formulated
      to support the growth of microorganisms, cells, or plants (National Cancer Institute
      Thesaurus).  A growth medium is a culture medium which has the disposition to
      encourage growth of particular bacteria to the exclusion of others in the same
      growth environment.  In this case, list the culture medium used to propagate
      the spike-in bacteria during preparation of spike-in inoculum. This field accepts
      terms listed under microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067).
      If the proper descriptor is not listed please use text to describe the spike
      in growth media
    title: spike-in growth medium
    examples:
    - value: LB broth [MCO:0000036]
    from_schema: https://w3id.org/mixs
    keywords:
    - growth
    - spike
    slot_uri: MIXS:0001169
    alias: spikein_growth_med
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    multivalued: 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
  spikein_strain:
    name: spikein_strain
    annotations:
      Expected_value:
        tag: Expected_value
        value: NCIT:C14250 or NCBI taxid or text
    description: Taxonomic information about the spike-in organism(s) at the strain
      level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250).
      This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy.
      Multiple terms can be separated by pipes
    title: spike-in microbial strain
    examples:
    - value: '169963'
    from_schema: https://w3id.org/mixs
    keywords:
    - microbial
    - spike
    string_serialization: '{termLabel} [{termID}]|{integer}'
    slot_uri: MIXS:0001170
    alias: spikein_strain
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    multivalued: true
  spikein_antibiotic:
    name: spikein_antibiotic
    annotations:
      Expected_value:
        tag: Expected_value
        value: drug name; concentration
    description: Antimicrobials used in research study to assess effects of exposure
      on microbiome of a specific site.  Please list antimicrobial, common name and/or
      class and concentration used for spike-in
    title: spike-in with antibiotics
    examples:
    - value: Tetracycline at 5 mg/ml
    from_schema: https://w3id.org/mixs
    keywords:
    - spike
    string_serialization: '{text} {integer}'
    slot_uri: MIXS:0001171
    alias: spikein_antibiotic
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    multivalued: true
  spikein_metal:
    name: spikein_metal
    annotations:
      Expected_value:
        tag: Expected_value
        value: heavy metal name or chemical symbol; concentration
    description: Heavy metals used in research study to assess effects of exposure
      on microbiome of a specific site.  Please list heavy metals and concentration
      used for spike-in
    title: spike-in with heavy metals
    examples:
    - value: Cd at 20 ppm
    from_schema: https://w3id.org/mixs
    keywords:
    - heavy
    - spike
    string_serialization: '{text} {integer}'
    slot_uri: MIXS:0001172
    alias: spikein_metal
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    multivalued: true
  timepoint:
    name: timepoint
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: hours or days
    description: Time point at which a sample or observation is made or taken from
      a biomaterial as measured from some reference point. Indicate the timepoint
      written in ISO 8601 format
    title: timepoint
    examples:
    - value: PT24H
    from_schema: https://w3id.org/mixs
    keywords:
    - time
    slot_uri: MIXS:0001173
    alias: timepoint
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
    structured_pattern:
      syntax: ^{duration}$
      interpolated: true
      partial_match: true
  water_frequency:
    name: water_frequency
    annotations:
      Expected_value:
        tag: Expected_value
        value: rate
      Preferred_unit:
        tag: Preferred_unit
        value: per day, per week, per month
    description: Number of water delivery events within a given period of time
    title: water delivery frequency
    examples:
    - value: 2 per day
    from_schema: https://w3id.org/mixs
    keywords:
    - delivery
    - frequency
    - water
    string_serialization: '{float}{unit}'
    slot_uri: MIXS:0001174
    alias: water_frequency
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    range: string
  water_pH:
    name: water_pH
    description: pH measurement of the sample, or liquid portion of sample, or aqueous
      phase of the fluid.
    title: water pH
    examples:
    - value: '7.2'
    from_schema: https://w3id.org/mixs
    keywords:
    - ph
    - water
    slot_uri: MIXS:0001175
    alias: water_pH
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: float
  water_source_shared:
    name: water_source_shared
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration
    description: Other users sharing access to the same water source. Multiple terms
      can be separated by one or more pipes
    title: water source shared
    examples:
    - value: no sharing
    from_schema: https://w3id.org/mixs
    keywords:
    - source
    - water
    string_serialization: '[multiple users, agricutural|multiple users, other|no sharing]'
    slot_uri: MIXS:0001176
    alias: water_source_shared
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    range: string
    multivalued: true
  enrichment_protocol:
    name: enrichment_protocol
    description: The microbiological workflow or protocol followed to test for the
      presence or enumeration of the target microbial analyte(s). Please provide a
      PubMed or DOI reference for published protocols
    title: enrichment protocol
    examples:
    - value: 'BAM Chapter 4: Enumeration of Escherichia coli and the Coliform Bacteria'
    from_schema: https://w3id.org/mixs
    keywords:
    - enrichment
    - protocol
    slot_uri: MIXS:0001177
    alias: enrichment_protocol
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: true
  food_quality_date:
    name: food_quality_date
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration, date
    description: The date recommended for the use of the product while at peak quality,
      this date is not a reflection of safety unless used on infant formula this date
      is not a reflection of safety and is typically labeled on a food product as
      "best if used by," best by," "use by," or "freeze by."
    title: food quality date
    examples:
    - value: best by 2020-05-24
    from_schema: https://w3id.org/mixs
    keywords:
    - date
    - food
    - quality
    string_serialization: '[best by|best if used by|freeze by|use by]; date'
    slot_uri: MIXS:0001178
    alias: food_quality_date
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  IFSAC_category:
    name: IFSAC_category
    annotations:
      Expected_value:
        tag: Expected_value
        value: IFSAC term
    description: 'The IFSAC food categorization scheme has five distinct levels to
      which foods can be assigned, depending upon the type of food. First, foods are
      assigned to one of four food groups (aquatic animals, land animals, plants,
      and other). Food groups include increasingly specific food categories; dairy,
      eggs, meat and poultry, and game are in the land animal food group, and the
      category meat and poultry is further subdivided into more specific categories
      of meat (beef, pork, other meat) and poultry (chicken, turkey, other poultry).
      Finally, foods are differentiated by differences in food processing (such as
      pasteurized fluid dairy products, unpasteurized fluid dairy products, pasteurized
      solid and semi-solid dairy products, and unpasteurized solid and semi-solid
      dairy products. An IFSAC food category chart is available from https://www.cdc.gov/foodsafety/ifsac/projects/food-categorization-scheme.html
      PMID: 28926300'
    title: Interagency Food Safety Analytics Collaboration (IFSAC) category
    examples:
    - value: Plants:Produce:Vegetables:Herbs:Dried Herbs
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    slot_uri: MIXS:0001179
    alias: IFSAC_category
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
    multivalued: true
  animal_housing:
    name: animal_housing
    description: Description of the housing system of the livestock. This field accepts
      terms listed under terrestrial management housing system (http://opendata.inra.fr/EOL/EOL_0001605)
    title: animal housing system
    examples:
    - value: pen rearing system [EOL:0001636]
    from_schema: https://w3id.org/mixs
    keywords:
    - animal
    slot_uri: MIXS:0001180
    alias: animal_housing
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    range: string
    multivalued: 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
  cult_isol_date:
    name: cult_isol_date
    description: The datetime marking the end of a process in which a sample yields
      a positive result for the target microbial analyte(s) in the form of an isolated
      colony or colonies
    title: culture isolation date
    examples:
    - value: '2018-05-11T10:00:00+01:00'
    from_schema: https://w3id.org/mixs
    keywords:
    - culture
    - date
    - isolation
    slot_uri: MIXS:0001181
    alias: cult_isol_date
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: datetime
  food_clean_proc:
    name: food_clean_proc
    description: The process of cleaning food to separate other environmental materials
      from the food source. Multiple terms can be separated by pipes
    title: food cleaning process
    examples:
    - value: rinsed with water
      description: was rinsed with water|scrubbed with brush
    - value: scrubbed with brush
      description: was rinsed with water|scrubbed with brush
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - process
    slot_uri: MIXS:0001182
    alias: food_clean_proc
    owner: MimagFoodFarmEnvironment
    domain_of:
    - FoodFarmEnvironment
    range: FoodCleanProcEnum
  misc_param:
    name: misc_param
    annotations:
      Expected_value:
        tag: Expected_value
        value: parameter name;measurement value
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    examples:
    - value: Bicarbonate ion concentration;2075 micromole per kilogram
    from_schema: https://w3id.org/mixs
    keywords:
    - parameter
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    alias: misc_param
    owner: MimagFoodFarmEnvironment
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
class_uri: MIXS:0010011_0016020