Combination: MimarksC combined with FoodAnimalAndAnimalFeed (MimarksCFoodAnimalAndAnimalFeed)

MIxS Data that comply with the MimarksC checklist and the FoodAnimalAndAnimalFeed Extension

Composition

MimarksC [Checklist] + FoodAnimalAndAnimalFeed [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:0000046	pcr_primers	0..1 recommended String	PCR primers that were used to amplify the sequence of the targeted gene, locu...
MIXS:0000038	nucl_acid_amp	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...
MIXS:0000045	target_subfragment	0..1 recommended String	Name of subfragment of a gene or locus
MIXS:0000113	temp	0..1 recommended String	Temperature of the sample at the time of sampling
MIXS:0000049	pcr_cond	0..1 recommended String	Description of reaction conditions and components of polymerase chain reactio...
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 String	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...
MIXS:0000003	isol_growth_condt	1 String	Publication reference in the form of pubmed ID (pmid), digital object identif...
MIXS:0000094	alt	0..1 recommended String	Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba...
MIXS:0000026	source_mat_id	* recommended String	A unique identifier assigned to a material sample (as defined by http://rs
MIXS:0000023	extrachrom_elements	0..1 Integer	Do plasmids exist of significant phenotypic consequence (e
MIXS:0000111	samp_vol_we_dna_ext	0..1 String	Volume (ml) or mass (g) of total collected sample processed for DNA extractio...
MIXS:0000015	rel_to_oxygen	0..1 recommended RelToOxygenEnum	Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ...
MIXS:0000002	samp_collect_device	0..1 String	The device used to collect an environmental sample
MIXS:0000028	biotic_relationship	0..1 recommended BioticRelationshipEnum	Description of relationship(s) between the subject organism and other organis...
MIXS:0000051	seq_quality_check	0..1 recommended SeqQualityCheckEnum	Indicate if the sequence has been called by automatic systems (none) or under...
MIXS:0000092	project_name	1 String	Name of the project within which the sequencing was organized
MIXS:0001321	neg_cont_type	0..1 recommended NegContTypeEnum	The substance or equipment used as a negative control in an investigation
MIXS:0000052	chimera_check	0..1 recommended String	Tool(s) used for chimera checking, including version number and parameters, t...
MIXS:0000032	trophic_level	0..1 recommended TrophicLevelEnum	Trophic levels are the feeding position in a food chain
MIXS:0001322	pos_cont_type	0..1 recommended String	The substance, mixture, product, or apparatus used to verify that a process w...
MIXS:0000020	subspecf_gen_lin	0..1 recommended String	Information about the genetic distinctness of the sequenced organism below th...
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:0000018	depth	0..1 recommended String	The vertical distance below local surface
MIXS:0001225	samp_collect_method	0..1 String	The method employed for collecting the sample
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:0000008	experimental_factor	* String	Variable aspects of an experiment design that can be used to describe an expe...
MIXS:0000044	target_gene	1 String	Targeted gene or locus name for marker gene studies
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: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:0000116	samp_store_dur	0..1 String	Duration for which the sample was stored
MIXS:0000325	pool_dna_extracts	0..1 String	Indicate whether multiple DNA extractions were mixed
MIXS:0000755	samp_store_loc	0..1 String	Location at which sample was stored, usually name of a specific freezer/room
MIXS:0001230	samp_transport_cont	0..1 SampTransportContEnum	Conatiner in which the sample was stored during transport
MIXS:0000754	perturbation	* String	Type of perturbation, e
MIXS:0001183	coll_site_geo_feat	1 String	Text or terms that describe the geographic feature where the food sample was ...
MIXS:0001207	food_origin	1 String	A reference to a place on the Earth, by its name or by its geographical locat...
MIXS:0001211	food_prod	1..* String	Descriptors of the food production system or of the agricultural environment ...
MIXS:0001184	food_product_type	1 String	A food product type is a class of food products that is differentiated by its...
MIXS:0001139	food_source	0..1 String	Type of plant or animal from which the food product or its major ingredient i...
MIXS:0001179	IFSAC_category	1..* String	The IFSAC food categorization scheme has five distinct levels to which foods ...
MIXS:0001144	intended_consumer	1..* String	Food consumer type, human or animal, for which the food product is produced a...
MIXS:0001151	samp_purpose	1 String	The reason that the sample was collected
MIXS:0001243	animal_am	0..1 String	The name(s) (generic or brand) of the antimicrobial(s) given to the food anim...
MIXS:0001244	animal_am_dur	0..1 String	The duration of time (days) that the antimicrobial was administered to the fo...
MIXS:0001245	animal_am_freq	0..1 Float	The frequency per day that the antimicrobial was administered to the food ani...
MIXS:0001246	animal_am_route	0..1 String	The route by which the antimicrobial is adminstered into the body of the food...
MIXS:0001247	animal_am_use	0..1 String	The prescribed intended use of or the condition treated by the antimicrobial ...
MIXS:0001248	animal_body_cond	0..1 AnimalBodyCondEnum	Body condition scoring is a production management tool used to evaluate overa...
MIXS:0001130	animal_diet	* String	If the isolate is from a food animal, the type of diet eaten by the food anim...
MIXS:0001113	animal_feed_equip	* String	Description of the feeding equipment used for livestock
MIXS:0001129	animal_group_size	0..1 Integer	The number of food animals of the same species that are maintained together a...
MIXS:0001180	animal_housing	* String	Description of the housing system of the livestock
MIXS:0001249	animal_sex	0..1 AnimalSexEnum	The sex and reproductive status of the food animal
MIXS:0001194	bacterial_density	0..1 String	Number of bacteria in sample, as defined by bacteria density (http://purl
MIXS:0001195	cons_food_stor_dur	0..1 String	The storage duration of the food commodity by the consumer, prior to onset of...
MIXS:0001196	cons_food_stor_temp	0..1 String	Temperature at which food commodity was stored by the consumer, prior to onse...
MIXS:0001197	cons_purch_date	0..1 Datetime	The date a food product was purchased by consumer
MIXS:0001198	cons_qty_purchased	0..1 String	The quantity of food purchased by consumer
MIXS:0001181	cult_isol_date	0..1 Datetime	The datetime marking the end of a process in which a sample yields a positive...
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:0001177	enrichment_protocol	0..1 String	The microbiological workflow or protocol followed to test for the presence or...
MIXS:0001200	food_additive	* String	A substance or substances added to food to maintain or improve safety and fre...
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:0001202	food_cooking_proc	* String	The transformation of raw food by the application of heat
MIXS:0001203	food_dis_point	* String	A reference to a place on the Earth, by its name or by its geographical locat...
MIXS:0001204	food_dis_point_city	* String	A reference to a place on the Earth, by its name or by its geographical locat...
MIXS:0001205	food_ingredient	* String	In this field, please list individual ingredients for multi-component food [F...
MIXS:0001208	food_pack_capacity	0..1 String	The maximum number of product units within a package
MIXS:0001209	food_pack_integrity	* String	A term label and term id to describe the state of the packing material and te...
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:0001210	food_prior_contact	* String	The material the food contacted (e
MIXS:0001212	food_prod_synonym	* String	Other names by which the food product is known by (e
MIXS:0001213	food_product_qual	0..1 String	Descriptors for describing food visually or via other senses, which is useful...
MIXS:0001178	food_quality_date	0..1 String	The date recommended for the use of the product while at peak quality, this d...
MIXS:0001251	food_source_age	0..1 String	The age of the food source host organim
MIXS:0001214	food_trace_list	0..1 FoodTraceListEnum	The FDA is proposing to establish additional traceability recordkeeping requi...
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:0001140	food_treat_proc	* String	Used to specifically characterize a food product based on the treatment or pr...
MIXS:0001215	HACCP_term	* String	Hazard Analysis Critical Control Points (HACCP) food safety terms; This field...
MIXS:0001145	library_prep_kit	0..1 String	Packaged kits (containing adapters, indexes, enzymes, buffers etc
MIXS:0001147	lot_number	* String	A distinctive alpha-numeric identification code assigned by the manufacturer ...
MIXS:0001216	microb_cult_med	0..1 String	A culture medium used to select for, grow, and maintain prokaryotic microorga...
MIXS:0001149	part_plant_animal	* String	The anatomical part of the organism being involved in food production or cons...
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:0001226	samp_rep_biol	0..1 String	Measurements of biologically distinct samples that show biological variation
MIXS:0001227	samp_rep_tech	0..1 String	Repeated measurements of the same sample that show independent measures of th...
MIXS:0001154	samp_source_mat_cat	0..1 String	This is the scientific role or category that the subject organism or material...
MIXS:0001228	samp_stor_device	0..1 String	The container used to store the sample
MIXS:0001229	samp_stor_media	0..1 String	The liquid that is added to the sample collection device prior to sampling
MIXS:0001231	samp_transport_dur	0..1 String	The duration of time from when the sample was collected until processed
MIXS:0001232	samp_transport_temp	0..1 String	Temperature at which sample was transported, e
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:0001235	spikein_AMR	* String	Qualitative description of a microbial response to antimicrobial agents
MIXS:0001171	spikein_antibiotic	* String	Antimicrobials used in research study to assess effects of exposure on microb...
MIXS:0001169	spikein_growth_med	* String	A liquid or gel containing nutrients, salts, and other factors formulated to ...
MIXS:0001172	spikein_metal	* String	Heavy metals used in research study to assess effects of exposure on microbio...
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:0001170	spikein_strain	* String	Taxonomic information about the spike-in organism(s) at the strain level
MIXS:0001236	study_design	* String	A plan specification comprised of protocols (which may specify how and what k...
MIXS:0001237	study_inc_dur	0..1 String	Sample incubation duration if unpublished or unvalidated method is used
MIXS:0001238	study_inc_temp	0..1 String	Sample incubation temperature if unpublished or unvalidated method is used
MIXS:0001239	study_timecourse	0..1 String	For time-course research studies involving samples of the food commodity, ind...
MIXS:0001240	study_tmnt	* String	A process in which the act is intended to modify or alter some other material...
MIXS:0001173	timepoint	0..1 String	Time point at which a sample or observation is made or taken from a biomateri...
MIXS:0000752	misc_param	* String	Any other measurement performed or parameter collected, that is not listed he...

LinkML Source

Direct

name: MimarksCFoodAnimalAndAnimalFeed
description: MIxS Data that comply with the MimarksC checklist and the FoodAnimalAndAnimalFeed
  Extension
title: MimarksC combined with FoodAnimalAndAnimalFeed
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: FoodAnimalAndAnimalFeed
mixins:
- MimarksC
class_uri: MIXS:0010009_0016019

Induced

name: MimarksCFoodAnimalAndAnimalFeed
description: MIxS Data that comply with the MimarksC checklist and the FoodAnimalAndAnimalFeed
  Extension
title: MimarksC combined with FoodAnimalAndAnimalFeed
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: FoodAnimalAndAnimalFeed
mixins:
- MimarksC
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: MimarksCFoodAnimalAndAnimalFeed
    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
  pcr_primers:
    name: pcr_primers
    annotations:
      Expected_value:
        tag: Expected_value
        value: 'FWD: forward primer sequence;REV:reverse primer sequence'
    description: PCR primers that were used to amplify the sequence of the targeted
      gene, locus or subfragment. This field should contain all the primers used for
      a single PCR reaction if multiple forward or reverse primers are present in
      a single PCR reaction. The primer sequence should be reported in uppercase letters
    title: pcr primers
    examples:
    - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - pcr
    string_serialization: FWD:{dna};REV:{dna}
    slot_uri: MIXS:0000046
    alias: pcr_primers
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  nucl_acid_amp:
    name: nucl_acid_amp
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the enzymatic amplification (PCR,
      TMA, NASBA) of specific nucleic acids
    title: nucleic acid amplification
    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: MimarksCFoodAnimalAndAnimalFeed
    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
  target_subfragment:
    name: target_subfragment
    description: Name of subfragment of a gene or locus. Important to e.g. identify
      special regions on marker genes like V6 on 16S rRNA
    title: target subfragment
    examples:
    - value: V6, V9, ITS
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - target
    slot_uri: MIXS:0000045
    alias: target_subfragment
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MimarksC
    - MimarksS
    - 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: MimarksCFoodAnimalAndAnimalFeed
    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
  pcr_cond:
    name: pcr_cond
    annotations:
      Expected_value:
        tag: Expected_value
        value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
          elongation:degrees_minutes;total cycles
    description: Description of reaction conditions and components of polymerase chain
      reaction performed during library preparation.
    title: pcr conditions
    examples:
    - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35
    - value: initial denaturation:94degC_1.5min
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - condition
    - pcr
    string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
      elongation:degrees_minutes;total cycles
    slot_uri: MIXS:0000049
    alias: pcr_cond
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  nucl_acid_ext:
    name: nucl_acid_ext
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the material separation to recover
      the nucleic acid fraction from a sample
    title: nucleic acid extraction
    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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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
  isol_growth_condt:
    name: isol_growth_condt
    description: Publication reference in the form of pubmed ID (pmid), digital object
      identifier (doi) or url for isolation and growth condition specifications of
      the organism/material
    title: isolation and growth condition
    examples:
    - value: doi:10.1016/j.syapm.2018.01.009
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - condition
    - growth
    - isolation
    slot_uri: MIXS:0000003
    alias: isol_growth_condt
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - MimarksC
    - Agriculture
    range: string
    required: 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
  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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - HostAssociated
    - MiscellaneousNaturalOrArtificialEnvironment
    - SymbiontAssociated
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  source_mat_id:
    name: source_mat_id
    annotations:
      Expected_value:
        tag: Expected_value
        value: 'for cultures of microorganisms: identifiers for two culture collections;
          for other material a unique arbitrary identifer'
    description: A unique identifier assigned to a material sample (as defined by
      http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
      digital record of a material sample) used for extracting nucleic acids, and
      subsequent sequencing. The identifier can refer either to the original material
      collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
      /bio_material, or /culture_collection may or may not share the same value as
      the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
      may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
      sampled tissue with the same identifier. However, the /culture_collection qualifier
      may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
      would refer to an identifier from some derived culture from which the nucleic
      acids were extracted (e.g. xatc123 or ark:/2154/R2)
    title: source material identifiers
    examples:
    - value: MPI012345
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - identifier
    - material
    - source
    slot_uri: MIXS:0000026
    alias: source_mat_id
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - SymbiontAssociated
    range: string
    recommended: true
    multivalued: true
  extrachrom_elements:
    name: extrachrom_elements
    description: Do plasmids exist of significant phenotypic consequence (e.g. ones
      that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids
      (borrelia has 15+ plasmids)
    title: extrachromosomal elements
    examples:
    - value: '5'
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000023
    alias: extrachrom_elements
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MimarksC
    range: integer
  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: MimarksCFoodAnimalAndAnimalFeed
    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
  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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    range: RelToOxygenEnum
    recommended: true
  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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  biotic_relationship:
    name: biotic_relationship
    description: Description of relationship(s) between the subject organism and other
      organism(s) it is associated with. E.g., parasite on species X; mutualist with
      species Y. The target organism is the subject of the relationship, and the other
      organism(s) is the object
    title: observed biotic relationship
    examples:
    - value: free living
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - observed
    - relationship
    slot_uri: MIXS:0000028
    alias: biotic_relationship
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - MimarksC
    - Miuvig
    - Agriculture
    range: BioticRelationshipEnum
    recommended: true
  seq_quality_check:
    name: seq_quality_check
    annotations:
      Expected_value:
        tag: Expected_value
        value: none or manually edited
    description: Indicate if the sequence has been called by automatic systems (none)
      or undergone a manual editing procedure (e.g. by inspecting the raw data or
      chromatograms). Applied only for sequences that are not submitted to SRA,ENA
      or DRA
    title: sequence quality check
    examples:
    - value: none
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - quality
    slot_uri: MIXS:0000051
    alias: seq_quality_check
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: SeqQualityCheckEnum
    recommended: 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: MimarksCFoodAnimalAndAnimalFeed
    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
  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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: NegContTypeEnum
    recommended: true
  chimera_check:
    name: chimera_check
    description: Tool(s) used for chimera checking, including version number and parameters,
      to discover and remove chimeric sequences. A chimeric sequence is comprised
      of two or more phylogenetically distinct parent sequences
    title: chimera check software
    examples:
    - value: uchime;v4.1;default parameters
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    slot_uri: MIXS:0000052
    alias: chimera_check
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  trophic_level:
    name: trophic_level
    description: Trophic levels are the feeding position in a food chain. Microbes
      can be a range of producers (e.g. chemolithotroph)
    title: trophic level
    examples:
    - value: heterotroph
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - level
    slot_uri: MIXS:0000032
    alias: trophic_level
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MimarksC
    - Agriculture
    range: TrophicLevelEnum
    recommended: true
  pos_cont_type:
    name: pos_cont_type
    description: The substance, mixture, product, or apparatus used to verify that
      a process which is part of an investigation delivers a true positive
    title: positive control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - type
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    alias: pos_cont_type
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    recommended: true
  subspecf_gen_lin:
    name: subspecf_gen_lin
    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 sequenced organism
      below the subspecies level, e.g., serovar, serotype, biotype, ecotype, 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: subspecific genetic lineage
    examples:
    - value: serovar:Newport
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - lineage
    string_serialization: '{rank name}:{text}'
    slot_uri: MIXS:0000020
    alias: subspecf_gen_lin
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - MimarksC
    - FoodFoodProductionFacility
    range: string
    recommended: true
  env_local_scale:
    name: env_local_scale
    annotations:
      Expected_value:
        tag: Expected_value
        value: Environmental entities having causal influences upon the entity at
          time of sampling
    description: 'Report the entity or entities which are in the sample or specimen
      s local vicinity and which you believe have significant causal influences on
      your sample or specimen. We recommend using EnvO terms which are of smaller
      spatial grain than your entry for env_broad_scale. Terms, such as anatomical
      sites, from other OBO Library ontologies which interoperate with EnvO (e.g.
      UBERON) are accepted in this field. EnvO documentation about how to use the
      field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: local environmental context
    examples:
    - value: hillside [ENVO:01000333]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - context
    - environmental
    slot_uri: MIXS:0000013
    alias: env_local_scale
    owner: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: 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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_collect_method:
    name: samp_collect_method
    description: The method employed for collecting the sample
    title: sample collection method
    examples:
    - value: swabbing
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    - sample
    slot_uri: MIXS:0001225
    alias: samp_collect_method
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - 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
  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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    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
  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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  target_gene:
    name: target_gene
    description: Targeted gene or locus name for marker gene studies
    title: target gene
    examples:
    - value: 16S rRNA, 18S rRNA, nif, amoA, rpo
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - target
    slot_uri: MIXS:0000044
    alias: target_gene
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    required: true
  associated_resource:
    name: associated_resource
    annotations:
      Expected_value:
        tag: Expected_value
        value: reference to resource
    description: A related resource that is referenced, cited, or otherwise associated
      to the sequence
    title: relevant electronic resources
    examples:
    - value: http://www.earthmicrobiome.org/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - resource
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000091
    alias: associated_resource
    owner: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    multivalued: true
  organism_count:
    name: organism_count
    annotations:
      Expected_value:
        tag: Expected_value
        value: organism name;measurement value;enumeration
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_store_dur:
    name: samp_store_dur
    description: Duration for which the sample was stored. Indicate the duration for
      which the sample was stored written in ISO 8601 format
    title: sample storage duration
    examples:
    - value: P1Y6M
    from_schema: https://w3id.org/mixs
    keywords:
    - duration
    - period
    - sample
    - storage
    slot_uri: MIXS:0000116
    alias: samp_store_dur
    owner: MimarksCFoodAnimalAndAnimalFeed
    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
  pool_dna_extracts:
    name: pool_dna_extracts
    annotations:
      Expected_value:
        tag: Expected_value
        value: pooling status;number of pooled extracts
      Preferred_unit:
        tag: Preferred_unit
        value: gram, milliliter, microliter
    description: Indicate whether multiple DNA extractions were mixed. If the answer
      yes, the number of extracts that were pooled should be given
    title: pooling of DNA extracts (if done)
    examples:
    - value: yes, 5
    from_schema: https://w3id.org/mixs
    keywords:
    - dna
    - pooling
    string_serialization: '{boolean},{integer}'
    slot_uri: MIXS:0000325
    alias: pool_dna_extracts
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - Soil
    range: string
  samp_store_loc:
    name: samp_store_loc
    annotations:
      Expected_value:
        tag: Expected_value
        value: location name
    description: Location at which sample was stored, usually name of a specific freezer/room
    title: sample storage location
    examples:
    - value: Freezer no:5
    from_schema: https://w3id.org/mixs
    keywords:
    - location
    - sample
    - storage
    slot_uri: MIXS:0000755
    alias: samp_store_loc
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
  samp_transport_cont:
    name: samp_transport_cont
    description: Conatiner in which the sample was stored during transport. Indicate
      the location name
    title: sample transport  container
    examples:
    - value: cooler
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - transport
    slot_uri: MIXS:0001230
    alias: samp_transport_cont
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: SampTransportContEnum
  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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  coll_site_geo_feat:
    name: coll_site_geo_feat
    annotations:
      Expected_value:
        tag: Expected_value
        value: ENVO:00000002 or ENVO:00000070
    description: 'Text or terms that describe the geographic feature where the food
      sample was obtained by the researcher. This field accepts selected terms listed
      under the following ontologies: anthropogenic geographic feature (http://purl.obolibrary.org/obo/ENVO_00000002),
      for example agricultural fairground [ENVO:01000986]; garden [ENVO:00000011}
      or any of its subclasses; market [ENVO:01000987]; water well [ENVO:01000002];
      or human construction (http://purl.obolibrary.org/obo/ENVO_00000070)'
    title: collection site geographic feature
    examples:
    - value: farm [ENVO:00000078]
    from_schema: https://w3id.org/mixs
    keywords:
    - feature
    - geographic
    - site
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001183
    alias: coll_site_geo_feat
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
  food_origin:
    name: food_origin
    description: A reference to a place on the Earth, by its name or by its geographical
      location that describes the origin of the food commodity, either in terms of
      its cultivation or production. This field accepts terms listed under geographic
      location (http://purl.obolibrary.org/obo/GAZ_00000448)
    title: food product origin geographic location
    examples:
    - value: 'USA: Delmarva, Peninsula'
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - geographic
    - location
    - product
    slot_uri: MIXS:0001207
    alias: food_origin
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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
  food_prod:
    name: food_prod
    description: Descriptors of the food production system or of the agricultural
      environment and growing conditions related to the farm production system, such
      as wild caught, organic, free-range, industrial, dairy, beef,  domestic or cultivated
      food production. This field accepts terms listed under food production (http://purl.obolibrary.org/obo/FOODON_03530206).
      Multiple terms may apply and can be separated by pipes
    title: food production system characteristics
    examples:
    - value: organic plant cultivation [FOODON:03530253]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - production
    slot_uri: MIXS:0001211
    alias: food_prod
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
    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_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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: 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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - 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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
    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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
    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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
  animal_am:
    name: animal_am
    description: The name(s) (generic or brand) of the antimicrobial(s) given to the
      food animal within the last 30 days
    title: food animal antimicrobial
    examples:
    - value: tetracycline
    from_schema: https://w3id.org/mixs
    keywords:
    - animal
    - antimicrobial
    - food
    slot_uri: MIXS:0001243
    alias: animal_am
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    range: string
  animal_am_dur:
    name: animal_am_dur
    description: The duration of time (days) that the antimicrobial was administered
      to the food animal
    title: food animal antimicrobial duration
    examples:
    - value: 3 days
    from_schema: https://w3id.org/mixs
    keywords:
    - animal
    - antimicrobial
    - duration
    - food
    - period
    slot_uri: MIXS:0001244
    alias: animal_am_dur
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    range: string
    structured_pattern:
      syntax: ^{float} days$
      interpolated: true
      partial_match: true
  animal_am_freq:
    name: animal_am_freq
    description: The frequency per day that the antimicrobial was administered to
      the food animal
    title: food animal antimicrobial frequency
    examples:
    - value: '1.5'
    from_schema: https://w3id.org/mixs
    keywords:
    - animal
    - antimicrobial
    - food
    - frequency
    slot_uri: MIXS:0001245
    alias: animal_am_freq
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    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
  animal_am_route:
    name: animal_am_route
    description: The route by which the antimicrobial is adminstered into the body
      of the food animal
    title: food animal antimicrobial route of administration
    examples:
    - value: oral-feed
    from_schema: https://w3id.org/mixs
    keywords:
    - administration
    - animal
    - antimicrobial
    - food
    - route
    slot_uri: MIXS:0001246
    alias: animal_am_route
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    range: string
  animal_am_use:
    name: animal_am_use
    description: The prescribed intended use of or the condition treated by the antimicrobial
      given to the food animal by any route of administration
    title: food animal antimicrobial intended use
    examples:
    - value: shipping fever
    from_schema: https://w3id.org/mixs
    keywords:
    - animal
    - antimicrobial
    - food
    - use
    slot_uri: MIXS:0001247
    alias: animal_am_use
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    range: string
  animal_body_cond:
    name: animal_body_cond
    description: Body condition scoring is a production management tool used to evaluate
      overall health and nutritional needs of a food animal. Because there are different
      scoring systems, this field is restricted to three categories
    title: food animal body condition
    examples:
    - value: under conditioned
    from_schema: https://w3id.org/mixs
    keywords:
    - animal
    - body
    - condition
    - food
    slot_uri: MIXS:0001248
    alias: animal_body_cond
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    range: AnimalBodyCondEnum
  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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    range: string
    multivalued: 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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    range: string
    multivalued: true
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    range: integer
  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: MimarksCFoodAnimalAndAnimalFeed
    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
  animal_sex:
    name: animal_sex
    description: The sex and reproductive status of the food animal
    title: food animal source sex category
    examples:
    - value: castrated male
    from_schema: https://w3id.org/mixs
    keywords:
    - animal
    - food
    - source
    slot_uri: MIXS:0001249
    alias: animal_sex
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    range: AnimalSexEnum
  bacterial_density:
    name: bacterial_density
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: colony forming units per milliliter; colony forming units per gram
          of dry weight
    description: Number of bacteria in sample, as defined by bacteria density (http://purl.obolibrary.org/obo/GENEPIO_0000043)
    title: bacteria density
    examples:
    - value: 10 colony forming units per gram dry weight
    from_schema: https://w3id.org/mixs
    keywords:
    - density
    slot_uri: MIXS:0001194
    alias: bacterial_density
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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
  cons_food_stor_dur:
    name: cons_food_stor_dur
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: hours or days
    description: The storage duration of the food commodity by the consumer, prior
      to onset of illness or sample collection.  Indicate the timepoint written in
      ISO 8601 format
    title: food stored by consumer (storage duration)
    examples:
    - value: P5D
    from_schema: https://w3id.org/mixs
    keywords:
    - consumer
    - duration)
    - food
    - storage
    slot_uri: MIXS:0001195
    alias: cons_food_stor_dur
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - 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
  cons_food_stor_temp:
    name: cons_food_stor_temp
    annotations:
      Expected_value:
        tag: Expected_value
        value: text or measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature at which food commodity was stored by the consumer, prior
      to onset of illness or sample collection
    title: food stored by consumer (storage temperature)
    examples:
    - value: 4 degree Celsius
    from_schema: https://w3id.org/mixs
    keywords:
    - consumer
    - food
    - storage
    - temperature
    string_serialization: '{float} {unit}|{text}'
    slot_uri: MIXS:0001196
    alias: cons_food_stor_temp
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodHumanFoods
    range: string
  cons_purch_date:
    name: cons_purch_date
    description: The date a food product was purchased by consumer
    title: purchase date
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    from_schema: https://w3id.org/mixs
    keywords:
    - date
    slot_uri: MIXS:0001197
    alias: cons_purch_date
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodHumanFoods
    range: datetime
  cons_qty_purchased:
    name: cons_qty_purchased
    description: The quantity of food purchased by consumer
    title: quantity purchased
    examples:
    - value: 5 cans
    from_schema: https://w3id.org/mixs
    keywords:
    - quantity
    slot_uri: MIXS:0001198
    alias: cons_qty_purchased
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodHumanFoods
    range: string
    pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{integer} {text}$
      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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: datetime
  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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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: MimarksCFoodAnimalAndAnimalFeed
    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_additive:
    name: food_additive
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03412972
    description: A substance or substances added to food to maintain or improve safety
      and freshness, to improve or maintain nutritional value, or improve taste, texture
      and appearance.  This field accepts terms listed under food additive (http://purl.obolibrary.org/obo/FOODON_03412972).
      Multiple terms can be separated by one or more pipes, but please consider limiting
      this list to the top 5 ingredients listed in order as on the food label.  See
      also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors
    title: food additive
    examples:
    - value: xanthan gum [FOODON:03413321]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001200
    alias: food_additive
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  food_cooking_proc:
    name: food_cooking_proc
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03450002
    description: The transformation of raw food by the application of heat. This field
      accepts terms listed under food cooking (http://purl.obolibrary.org/obo/FOODON_03450002)
    title: food cooking process
    examples:
    - value: food blanching [FOODON:03470175]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - process
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001202
    alias: food_cooking_proc
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  food_dis_point:
    name: food_dis_point
    description: 'A reference to a place on the Earth, by its name or by its geographical
      location that refers to a distribution point along the food chain. This field
      accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448).
      Reference: Adam Diamond, James Barham. Moving Food Along the Value Chain: Innovations
      in Regional Food Distribution. U.S. Dept. of Agriculture, Agricultural Marketing
      Service. Washington, DC. March 2012. http://dx.doi.org/10.9752/MS045.03-2012'
    title: food distribution point geographic location
    examples:
    - value: 'USA: Delmarva, Peninsula'
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - geographic
    - location
    slot_uri: MIXS:0001203
    alias: food_dis_point
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: 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
  food_dis_point_city:
    name: food_dis_point_city
    annotations:
      Expected_value:
        tag: Expected_value
        value: GAZ:00000448
    description: 'A reference to a place on the Earth, by its name or by its geographical
      location that refers to a distribution point along the food chain. This field
      accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448).
      Reference: Adam Diamond, James Barham. Moving Food Along the Value Chain: Innovations
      in Regional Food Distribution. U.S. Dept. of Agriculture, Agricultural Marketing
      Service. Washington, DC. March 2012. http://dx.doi.org/10.9752/MS045.03-2012'
    title: food distribution point geographic location (city)
    examples:
    - value: Atlanta[GAZ:00004445]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - geographic
    - location
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001204
    alias: food_dis_point_city
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    range: string
    multivalued: true
  food_ingredient:
    name: food_ingredient
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON
    description: In this field, please list individual ingredients for multi-component
      food [FOODON:00002501] and simple foods that is not captured in food_type.  Please
      use terms that are present in FoodOn.  Multiple terms can be separated by one
      or more pipes |, but please consider limiting this list to the top 5 ingredients
      listed in order as on the food label.  See also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors
    title: food ingredient
    examples:
    - value: bean (whole) [FOODON:00002753]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - ingredient
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001205
    alias: food_ingredient
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  food_pack_capacity:
    name: food_pack_capacity
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: grams
    description: The maximum number of product units within a package
    title: food package capacity
    examples:
    - value: 454 grams
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - package
    slot_uri: MIXS:0001208
    alias: food_pack_capacity
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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
  food_pack_integrity:
    name: food_pack_integrity
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03530218
    description: A term label and term id to describe the state of the packing material
      and text to explain the exact condition.  This field accepts terms listed under
      food packing medium integrity (http://purl.obolibrary.org/obo/FOODON_03530218)
    title: food packing medium integrity
    examples:
    - value: food packing medium compromised [FOODON:00002517]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001209
    alias: food_pack_integrity
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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: packed in fruit juice [FOODON:03480039]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001134
    alias: food_pack_medium
    owner: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  food_prior_contact:
    name: food_prior_contact
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03530077
    description: The material the food contacted (e.g., was processed in) prior to
      packaging. This field accepts terms listed under material of contact prior to
      food packaging (http://purl.obolibrary.org/obo/FOODON_03530077). If the proper
      descriptor is not listed please use text to describe the material of contact
      prior to food packaging
    title: material of contact prior to food packaging
    examples:
    - value: processed in stainless steel container [FOODON:03530081]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - material
    - prior
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001210
    alias: food_prior_contact
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  food_prod_synonym:
    name: food_prod_synonym
    description: Other names by which the food product is known by (e.g., regional
      or non-English names)
    title: food product synonym
    examples:
    - value: pinot gris
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - product
    slot_uri: MIXS:0001212
    alias: food_prod_synonym
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  food_product_qual:
    name: food_product_qual
    description: Descriptors for describing food visually or via other senses, which
      is useful for tasks like food inspection where little prior knowledge of how
      the food came to be is available. Some terms like "food (frozen)" are both a
      quality descriptor and the output of a process. This field accepts terms listed
      under food product by quality (http://purl.obolibrary.org/obo/FOODON_00002454)
    title: food product by quality
    examples:
    - value: raw [FOODON:03311126]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - product
    - quality
    slot_uri: MIXS:0001213
    alias: food_product_qual
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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
  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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  food_source_age:
    name: food_source_age
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: days
    description: The age of the food source host organim. Depending on the type of
      host organism, age may be more appropriate to report in days, weeks, or years
    title: food source age
    comments:
    - ISO 8601 period or measurement value?
    examples:
    - value: 6 months
    from_schema: https://w3id.org/mixs
    keywords:
    - age
    - food
    - source
    slot_uri: MIXS:0001251
    alias: food_source_age
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    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
  food_trace_list:
    name: food_trace_list
    description: The FDA is proposing to establish additional traceability recordkeeping
      requirements (beyond what is already required in existing regulations) for persons
      who manufacture, process, pack, or hold foods the Agency has designated for
      inclusion on the Food Traceability List. The Food Traceability List (FTL) identifies
      the foods for which the additional traceability records described in the proposed
      rule would be required. The term  Food Traceability List  (FTL) refers not only
      to the foods specifically listed (https://www.fda.gov/media/142303/download),
      but also to any foods that contain listed foods as ingredients
    title: food traceability list category
    examples:
    - value: tropical tree fruits
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    slot_uri: MIXS:0001214
    alias: food_trace_list
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: FoodTraceListEnum
  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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  HACCP_term:
    name: HACCP_term
    description: Hazard Analysis Critical Control Points (HACCP) food safety terms;
      This field accepts terms listed under HACCP guide food safety term (http://purl.obolibrary.org/obo/FOODON_03530221)
    title: Hazard Analysis Critical Control Points (HACCP) guide food safety term
    examples:
    - value: tetrodotoxic poisoning [FOODON:03530249]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - term
    slot_uri: MIXS:0001215
    alias: HACCP_term
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - 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
  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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  microb_cult_med:
    name: microb_cult_med
    description: A culture medium used to select for, grow, and maintain prokaryotic
      microorganisms. Can be in either liquid (broth) or solidified (e.g. with agar)
      forms. 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 culture medium
    title: microbiological culture medium
    examples:
    - value: brain heart infusion agar [MICRO:0000566]
    from_schema: https://w3id.org/mixs
    keywords:
    - culture
    - microbiological
    slot_uri: MIXS:0001216
    alias: microb_cult_med
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    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
  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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  samp_rep_biol:
    name: samp_rep_biol
    description: Measurements of biologically distinct samples that show biological
      variation
    title: biological sample replicate
    examples:
    - value: 6 replicates
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    slot_uri: MIXS:0001226
    alias: samp_rep_biol
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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_rep_tech:
    name: samp_rep_tech
    description: Repeated measurements of the same sample that show independent measures
      of the noise associated with the equipment and the protocols
    title: technical sample replicate
    examples:
    - value: 10 replicates
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    slot_uri: MIXS:0001227
    alias: samp_rep_tech
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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_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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  samp_stor_device:
    name: samp_stor_device
    annotations:
      Expected_value:
        tag: Expected_value
        value: NCIT:C4318
    description: The container used to store the  sample. This field accepts terms
      listed under container (http://purl.obolibrary.org/obo/NCIT_C43186). If the
      proper descriptor is not listed please use text to describe the storage device
    title: sample storage device
    examples:
    - value: Whirl Pak sampling bag [GENEPIO:0002122]
    from_schema: https://w3id.org/mixs
    keywords:
    - device
    - sample
    - storage
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001228
    alias: samp_stor_device
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  samp_stor_media:
    name: samp_stor_media
    description: The liquid that is added to the sample collection device prior to
      sampling. If the sample is pre-hydrated, indicate the liquid media the sample
      is pre-hydrated with for storage purposes. 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 sample
      storage media
    title: sample storage media
    examples:
    - value: peptone water medium [MICRO:0000548]
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - storage
    slot_uri: MIXS:0001229
    alias: samp_stor_media
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    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
  samp_transport_dur:
    name: samp_transport_dur
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: days
    description: The duration of time from when the sample was collected until processed.
      Indicate the duration for which the sample was stored written in ISO 8601 format
    title: sample transport duration
    examples:
    - value: P10D
    from_schema: https://w3id.org/mixs
    keywords:
    - duration
    - period
    - sample
    - transport
    slot_uri: MIXS:0001231
    alias: samp_transport_dur
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - 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
  samp_transport_temp:
    name: samp_transport_temp
    annotations:
      Expected_value:
        tag: Expected_value
        value: text or measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature at which sample was transported, e.g. -20 or 4 degree
      Celsius
    title: sample transport temperature
    examples:
    - value: 4 degree Celsius
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - temperature
    - transport
    string_serialization: '{float} {unit} {text}'
    slot_uri: MIXS:0001232
    alias: samp_transport_temp
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - 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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    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_AMR:
    name: spikein_AMR
    annotations:
      Expected_value:
        tag: Expected_value
        value: measurement value ARO:3004299
    description: Qualitative description of a microbial response to antimicrobial
      agents. Bacteria may be susceptible or resistant to a broad range of antibiotic
      drugs or drug classes, with several intermediate states or phases. This field
      accepts terms under antimicrobial phenotype (http://purl.obolibrary.org/obo/ARO_3004299)
    title: antimicrobial phenotype of spike-in bacteria
    examples:
    - value: wild type [ARO:3004432]
    from_schema: https://w3id.org/mixs
    keywords:
    - antimicrobial
    - spike
    string_serialization: '{float} {unit};{termLabel} [{termID}]'
    slot_uri: MIXS:0001235
    alias: spikein_AMR
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - 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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    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_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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    multivalued: true
  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: MimarksCFoodAnimalAndAnimalFeed
    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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    multivalued: 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: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    multivalued: true
  study_design:
    name: study_design
    annotations:
      Expected_value:
        tag: Expected_value
        value: OBI:0500000
    description: A plan specification comprised of protocols (which may specify how
      and what kinds of data will be gathered) that are executed as part of an investigation
      and is realized during a study design execution. This field accepts terms under
      study design (http://purl.obolibrary.org/obo/OBI_0500000). If the proper descriptor
      is not listed please use text to describe the study design. Multiple terms can
      be separated by pipes
    title: study design
    examples:
    - value: in vitro design [OBI:0001285]
    from_schema: https://w3id.org/mixs
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001236
    alias: study_design
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  study_inc_dur:
    name: study_inc_dur
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: hours or days
    description: Sample incubation duration if unpublished or unvalidated method is
      used. Indicate the timepoint written in ISO 8601 format
    title: study incubation duration
    examples:
    - value: PT24H
    from_schema: https://w3id.org/mixs
    keywords:
    - duration
    - incubation
    - period
    slot_uri: MIXS:0001237
    alias: study_inc_dur
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - 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
  study_inc_temp:
    name: study_inc_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Sample incubation temperature if unpublished or unvalidated method
      is used
    title: study incubation temperature
    examples:
    - value: 37 degree Celsius
    from_schema: https://w3id.org/mixs
    keywords:
    - incubation
    - temperature
    slot_uri: MIXS:0001238
    alias: study_inc_temp
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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
  study_timecourse:
    name: study_timecourse
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: dpi
    description: For time-course research studies involving samples of the food commodity,
      indicate the total duration of the time-course study
    title: time-course duration
    examples:
    - value: 2 days post inoculation
    from_schema: https://w3id.org/mixs
    keywords:
    - duration
    - period
    - time
    slot_uri: MIXS:0001239
    alias: study_timecourse
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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
  study_tmnt:
    name: study_tmnt
    annotations:
      Expected_value:
        tag: Expected_value
        value: MCO:0000866
    description: A process in which the act is intended to modify or alter some other
      material entity.  From the study design, each treatment is comprised of one
      level of one or multiple factors. This field accepts terms listed under treatment
      (http://purl.obolibrary.org/obo/MCO_0000866). If the proper descriptor is not
      listed please use text to describe the study treatment. Multiple terms can be
      separated by one or more pipes
    title: study treatment
    examples:
    - value: Factor A|spike-in|levels high, medium, low
    from_schema: https://w3id.org/mixs
    keywords:
    - treatment
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001240
    alias: study_tmnt
    owner: MimarksCFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - 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: MimarksCFoodAnimalAndAnimalFeed
    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
  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: MimarksCFoodAnimalAndAnimalFeed
    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:0010009_0016019