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Combination: MimarksS combined with FoodFoodProductionFacility (MimarksSFoodFoodProductionFacility)

MIxS Data that comply with the MimarksS checklist and the FoodFoodProductionFacility Extension

Composition

MimarksS [Checklist] + FoodFoodProductionFacility [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:0000017 size_frac 0..1
String
Filtering pore size used in sample preparation
MIXS:0000043 lib_screen 0..1 recommended
String
Specific enrichment or screening methods applied before and/or after creating...
MIXS:0000038 nucl_acid_amp 0..1 recommended
String
A link to a literature reference, electronic resource or a standard operating...
MIXS:0000039 lib_size 0..1 recommended
Integer
Total number of clones in the library prepared for the project
MIXS:0000045 target_subfragment 0..1 recommended
String
Name of subfragment of a gene or locus
MIXS:0000047 mid 0..1 recommended
String
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe...
MIXS:0000113 temp 0..1 recommended
String
Temperature of the sample at the time of sampling
MIXS:0000037 nucl_acid_ext 0..1 recommended
String
A link to a literature reference, electronic resource or a standard operating...
MIXS:0000001 samp_size 0..1 recommended
String
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...
MIXS:0000094 alt 0..1 recommended
String
Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba...
MIXS:0000026 source_mat_id * recommended
String
A unique identifier assigned to a material sample (as defined by http://rs
MIXS:0000111 samp_vol_we_dna_ext 0..1
String
Volume (ml) or mass (g) of total collected sample processed for DNA extractio...
MIXS:0000040 lib_reads_seqd 0..1 recommended
Integer
Total number of clones sequenced from the library
MIXS:0000015 rel_to_oxygen 0..1
RelToOxygenEnum
Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ...
MIXS:0000002 samp_collect_device 0..1 recommended
String
The device used to collect an environmental sample
MIXS:0000051 seq_quality_check 0..1 recommended
SeqQualityCheckEnum
Indicate if the sequence has been called by automatic systems (none) or under...
MIXS:0000041 lib_layout 0..1 recommended
LibLayoutEnum
Specify whether to expect single, paired, or other configuration of reads
MIXS:0000012 env_broad_scale 1
String
Report the major environmental system the sample or specimen came from
MIXS:0000092 project_name 1
String
Name of the project within which the sequencing was organized
MIXS:0000042 lib_vector 0..1 recommended
String
Cloning vector type(s) used in construction of libraries
MIXS:0000048 adapters 0..1 recommended
String
Adapters provide priming sequences for both amplification and sequencing of t...
MIXS:0001321 neg_cont_type 0..1 recommended
NegContTypeEnum
The substance or equipment used as a negative control in an investigation
MIXS:0000058 assembly_software 0..1 recommended
String
Tool(s) used for assembly, including version number and parameters
MIXS:0000052 chimera_check 0..1 recommended
String
Tool(s) used for chimera checking, including version number and parameters, t...
MIXS:0001322 pos_cont_type 0..1 recommended
String
The substance, mixture, product, or apparatus used to verify that a process w...
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 recommended
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:0000049 pcr_cond 0..1 recommended
String
Description of reaction conditions and components of polymerase chain reactio...
MIXS:0000008 experimental_factor * recommended
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: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:0000124 air_temp 0..1
String
Temperature of the air at the time of sampling
MIXS:0000192 room_dim 0..1
String
The length, width and height of sampling room
MIXS:0000226 freq_clean 0..1
FreqCleanEnum
The number of times the sample location is cleaned
MIXS:0000244 samp_room_id 0..1
Integer
Sampling room number
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:0000758 surf_material 0..1
SurfMaterialEnum
Surface materials at the point of sampling
MIXS:0000764 indoor_surf 0..1
IndoorSurfEnum
Type of indoor surface
MIXS:0000775 avg_occup 0..1
Float
Daily average occupancy of room
MIXS:0000828 samp_floor 0..1
String
The floor of the building, where the sampling room is located
MIXS:0000859 genetic_mod 0..1
String
Genetic modifications of the genome of an organism, which may occur naturally...
MIXS:0001183 coll_site_geo_feat 1
String
Text or terms that describe the geographic feature where the food sample was ...
MIXS:0001154 samp_source_mat_cat 1
String
This is the scientific role or category that the subject organism or material...
MIXS:0000998 samp_type 1
String
The type of material from which the sample was obtained
MIXS:0001229 samp_stor_media 1
String
The liquid that is added to the sample collection device prior to sampling
MIXS:0001228 samp_stor_device 1
String
The container used to store the sample
MIXS:0001184 food_product_type 1
String
A food product type is a class of food products that is differentiated by its...
MIXS:0001179 IFSAC_category 1..*
String
The IFSAC food categorization scheme has five distinct levels to which foods ...
MIXS:0001213 food_product_qual 1
String
Descriptors for describing food visually or via other senses, which is useful...
MIXS:0001131 food_contact_surf 1..*
String
The specific container or coating materials in direct contact with the food
MIXS:0001252 facility_type *
FacilityTypeEnum
Establishment details about the type of facility where the sample was taken
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: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:0001224 num_samp_collect 0..1
String
The number of samples collected during the current sampling event
MIXS:0001147 lot_number *
String
A distinctive alpha-numeric identification code assigned by the manufacturer ...
MIXS:0001253 hygienic_area 0..1
String
The subdivision of areas within a food production facility according to hygie...
MIXS:0001254 env_monitoring_zone 0..1
String
An environmental monitoring zone is a formal designation as part of an enviro...
MIXS:0001255 area_samp_size 0..1
String
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...
MIXS:0001256 samp_surf_moisture *
SampSurfMoistureEnum
Degree of water held on a sampled surface
MIXS:0001257 samp_loc_condition 0..1
SampLocConditionEnum
The condition of the sample location at the time of sampling
MIXS:0001258 biocide_used *
String
Substance intended for preventing, neutralizing, destroying, repelling, or mi...
MIXS:0001259 ster_meth_samp_room *
String
The method used to sterilize the sampling room
MIXS:0001177 enrichment_protocol 0..1
String
The microbiological workflow or protocol followed to test for the presence or...
MIXS:0001119 cult_target *
String
The target microbial analyte in terms of investigation scope
MIXS:0001216 microb_cult_med 0..1
String
A culture medium used to select for, grow, and maintain prokaryotic microorga...
MIXS:0001173 timepoint 0..1
String
Time point at which a sample or observation is made or taken from a biomateri...
MIXS:0001194 bacterial_density 0..1
String
Number of bacteria in sample, as defined by bacteria density (http://purl
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:0000020 subspecf_gen_lin 0..1
String
Information about the genetic distinctness of the sequenced organism below th...
MIXS:0001153 samp_pooling *
String
Physical combination of several instances of like material, e
MIXS:0001151 samp_purpose 0..1
String
The reason that the sample was collected
MIXS:0001227 samp_rep_tech 0..1
String
Repeated measurements of the same sample that show independent measures of th...
MIXS:0001226 samp_rep_biol 0..1
String
Measurements of biologically distinct samples that show biological variation
MIXS:0001230 samp_transport_cont 0..1
SampTransportContEnum
Conatiner in which the sample was stored during transport
MIXS:0001236 study_design *
String
A plan specification comprised of protocols (which may specify how and what k...
MIXS:0001223 nucl_acid_ext_kit *
String
The name of the extraction kit used to recover the nucleic acid fraction of a...
MIXS:0001145 library_prep_kit 0..1
String
Packaged kits (containing adapters, indexes, enzymes, buffers etc
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:0001238 study_inc_temp 0..1
String
Sample incubation temperature if unpublished or unvalidated method is used
MIXS:0001237 study_inc_dur 0..1
String
Sample incubation duration 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:0001139 food_source 0..1
String
Type of plant or animal from which the food product or its major ingredient i...
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:0001207 food_origin 0..1
String
A reference to a place on the Earth, by its name or by its geographical locat...
MIXS:0001212 food_prod_synonym *
String
Other names by which the food product is known by (e
MIXS:0001200 food_additive *
String
A substance or substances added to food to maintain or improve safety and fre...
MIXS:0001214 food_trace_list 0..1
FoodTraceListEnum
The FDA is proposing to establish additional traceability recordkeeping requi...
MIXS:0001149 part_plant_animal *
String
The anatomical part of the organism being involved in food production or cons...
MIXS:0001205 food_ingredient *
String
In this field, please list individual ingredients for multi-component food [F...
MIXS:0001234 spec_intended_cons *
String
Food consumer type, human or animal, for which the food product is produced a...
MIXS:0001215 HACCP_term *
String
Hazard Analysis Critical Control Points (HACCP) food safety terms; This field...
MIXS:0001199 dietary_claim_use *
String
These descriptors are used either for foods intended for special dietary use ...
MIXS:0001201 food_allergen_label *
String
A label indication that the product contains a recognized allergen
MIXS:0001136 food_prod_char *
String
Descriptors of the food production system such as wild caught, free-range, or...
MIXS:prod_label_claims prod_label_claims *
String
Labeling claims containing descriptors such as wild caught, free-range, organ...
MIXS:0001206 food_name_status 0..1
String
A datum indicating that use of a food product name is regulated in some legal...
MIXS:0001135 food_preserv_proc *
String
The methods contributing to the prevention or retardation of microbial, enzym...
MIXS:0001202 food_cooking_proc *
String
The transformation of raw food by the application of heat
MIXS:0001140 food_treat_proc *
String
Used to specifically characterize a food product based on the treatment or pr...
MIXS:0001132 food_contain_wrap 0..1
String
Type of container or wrapping defined by the main container material, the con...
MIXS:0001208 food_pack_capacity 0..1
String
The maximum number of product units within a package
MIXS:0001134 food_pack_medium *
String
The medium in which the food is packed for preservation and handling or the m...
MIXS:0001210 food_prior_contact *
String
The material the food contacted (e
MIXS:0001211 food_prod *
String
Descriptors of the food production system or of the agricultural environment ...
MIXS:0001178 food_quality_date 0..1
String
The date recommended for the use of the product while at peak quality, this d...
MIXS:0001152 repository_name *
String
The name of the institution where the sample or DNA extract is held or "sampl...
MIXS:0001144 intended_consumer *
String
Food consumer type, human or animal, for which the food product is produced a...
MIXS:0001209 food_pack_integrity *
String
A term label and term id to describe the state of the packing material and te...
MIXS:0000752 misc_param *
String
Any other measurement performed or parameter collected, that is not listed he...

LinkML Source

Direct

name: MimarksSFoodFoodProductionFacility
description: MIxS Data that comply with the MimarksS checklist and the FoodFoodProductionFacility
  Extension
title: MimarksS combined with FoodFoodProductionFacility
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: FoodFoodProductionFacility
mixins:
- MimarksS
class_uri: MIXS:0010008_0016021

Induced

name: MimarksSFoodFoodProductionFacility
description: MIxS Data that comply with the MimarksS checklist and the FoodFoodProductionFacility
  Extension
title: MimarksS combined with FoodFoodProductionFacility
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: FoodFoodProductionFacility
mixins:
- MimarksS
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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  size_frac:
    name: size_frac
    annotations:
      Expected_value:
        tag: Expected_value
        value: filter size value range
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    examples:
    - value: 0-0.22 micrometer
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - fraction
    - size
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    alias: size_frac
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
  lib_screen:
    name: lib_screen
    annotations:
      Expected_value:
        tag: Expected_value
        value: screening strategy name
    description: Specific enrichment or screening methods applied before and/or after
      creating libraries
    title: library screening strategy
    examples:
    - value: enriched, screened, normalized
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000043
    alias: lib_screen
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - 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: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  lib_size:
    name: lib_size
    description: Total number of clones in the library prepared for the project
    title: library size
    examples:
    - value: '50'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    - size
    slot_uri: MIXS:0000039
    alias: lib_size
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    recommended: 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: MimarksSFoodFoodProductionFacility
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  mid:
    name: mid
    description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
      used to specifically tag unique samples in a sequencing run. Sequence should
      be reported in uppercase letters
    title: multiplex identifiers
    examples:
    - value: GTGAATAT
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - identifier
    slot_uri: MIXS:0000047
    alias: mid
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^[ACGTRKSYMWBHDVN]+$
    structured_pattern:
      syntax: ^{ambiguous_nucleotides}$
      interpolated: true
      partial_match: 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: MimarksSFoodFoodProductionFacility
    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
  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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  alt:
    name: alt
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric
      balloons and heights of places such as atmospheric layers and clouds. It is
      used to measure the height of an object which is above the earth's surface.
      In this context, the altitude measurement is the vertical distance between the
      earth's surface above sea level and the sampled position in the air
    title: altitude
    examples:
    - value: 100 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000094
    alias: alt
    owner: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - SymbiontAssociated
    range: string
    recommended: true
    multivalued: true
  samp_vol_we_dna_ext:
    name: samp_vol_we_dna_ext
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milliliter, gram, milligram, square centimeter
    description: 'Volume (ml) or mass (g) of total collected sample processed for
      DNA extraction. Note: total sample collected should be entered under the term
      Sample Size (MIXS:0000001)'
    title: sample volume or weight for DNA extraction
    examples:
    - value: 1500 milliliter
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - dna
    - sample
    - volume
    - weight
    slot_uri: MIXS:0000111
    alias: samp_vol_we_dna_ext
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  lib_reads_seqd:
    name: lib_reads_seqd
    description: Total number of clones sequenced from the library
    title: library reads sequenced
    examples:
    - value: '20'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000040
    alias: lib_reads_seqd
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    recommended: true
  rel_to_oxygen:
    name: rel_to_oxygen
    description: Is this organism an aerobe, anaerobe? Please note that aerobic and
      anaerobic are valid descriptors for microbial environments
    title: relationship to oxygen
    examples:
    - value: aerobe
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - oxygen
    - relationship
    slot_uri: MIXS:0000015
    alias: rel_to_oxygen
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    range: RelToOxygenEnum
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: SeqQualityCheckEnum
    recommended: true
  lib_layout:
    name: lib_layout
    description: Specify whether to expect single, paired, or other configuration
      of reads
    title: library layout
    examples:
    - value: paired
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000041
    alias: lib_layout
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: LibLayoutEnum
    recommended: 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: MimarksSFoodFoodProductionFacility
    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
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: true
  lib_vector:
    name: lib_vector
    annotations:
      Expected_value:
        tag: Expected_value
        value: vector
    description: Cloning vector type(s) used in construction of libraries
    title: library vector
    examples:
    - value: Bacteriophage P1
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000042
    alias: lib_vector
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  adapters:
    name: adapters
    description: Adapters provide priming sequences for both amplification and sequencing
      of the sample-library fragments. Both adapters should be reported; in uppercase
      letters
    title: adapters
    examples:
    - value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000048
    alias: adapters
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    structured_pattern:
      syntax: ^{adapter_A_DNA_sequence};{adapter_B_DNA_sequence}$
      interpolated: true
      partial_match: true
  neg_cont_type:
    name: neg_cont_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration or text
    description: The substance or equipment used as a negative control in an investigation
    title: negative control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - type
    slot_uri: MIXS:0001321
    alias: neg_cont_type
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: NegContTypeEnum
    recommended: true
  assembly_software:
    name: assembly_software
    description: Tool(s) used for assembly, including version number and parameters
    title: assembly software
    examples:
    - value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    slot_uri: MIXS:0000058
    alias: assembly_software
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  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: MimarksSFoodFoodProductionFacility
    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
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    recommended: true
  env_local_scale:
    name: env_local_scale
    annotations:
      Expected_value:
        tag: Expected_value
        value: Environmental entities having causal influences upon the entity at
          time of sampling
    description: 'Report the entity or entities which are in the sample or specimen
      s local vicinity and which you believe have significant causal influences on
      your sample or specimen. We recommend using EnvO terms which are of smaller
      spatial grain than your entry for env_broad_scale. Terms, such as anatomical
      sites, from other OBO Library ontologies which interoperate with EnvO (e.g.
      UBERON) are accepted in this field. EnvO documentation about how to use the
      field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: local environmental context
    examples:
    - value: hillside [ENVO:01000333]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - context
    - environmental
    slot_uri: MIXS:0000013
    alias: env_local_scale
    owner: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: true
  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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    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
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: 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: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    multivalued: true
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - Agriculture
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  samp_store_temp:
    name: samp_store_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature at which sample was stored, e.g. -80 degree Celsius
    title: sample storage temperature
    examples:
    - value: -80 degree Celsius
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - storage
    - temperature
    slot_uri: MIXS:0000110
    alias: samp_store_temp
    owner: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    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
  air_temp:
    name: air_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature of the air at the time of sampling
    title: air temperature
    examples:
    - value: 4 degree Celsius
    from_schema: https://w3id.org/mixs
    keywords:
    - air
    - temperature
    slot_uri: MIXS:0000124
    alias: air_temp
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - BuiltEnvironment
    - FoodFoodProductionFacility
    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
  room_dim:
    name: room_dim
    annotations:
      Expected_value:
        tag: Expected_value
        value: measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: The length, width and height of sampling room
    title: room dimensions
    examples:
    - value: 4 meter x 4 meter x 4 meter
    from_schema: https://w3id.org/mixs
    keywords:
    - dimensions
    - room
    string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'
    slot_uri: MIXS:0000192
    alias: room_dim
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - BuiltEnvironment
    - FoodFoodProductionFacility
    range: string
  freq_clean:
    name: freq_clean
    description: The number of times the sample location is cleaned. Frequency of
      cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually
    title: frequency of cleaning
    examples:
    - value: Daily
    from_schema: https://w3id.org/mixs
    keywords:
    - frequency
    slot_uri: MIXS:0000226
    alias: freq_clean
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - BuiltEnvironment
    - FoodFoodProductionFacility
    range: FreqCleanEnum
  samp_room_id:
    name: samp_room_id
    description: Sampling room number. This ID should be consistent with the designations
      on the building floor plans
    title: sampling room ID or name
    from_schema: https://w3id.org/mixs
    keywords:
    - identifier
    - room
    slot_uri: MIXS:0000244
    alias: samp_room_id
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - BuiltEnvironment
    - FoodFoodProductionFacility
    range: integer
  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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
  surf_material:
    name: surf_material
    description: Surface materials at the point of sampling
    title: surface material
    examples:
    - value: wood
    from_schema: https://w3id.org/mixs
    keywords:
    - material
    - surface
    slot_uri: MIXS:0000758
    alias: surf_material
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - BuiltEnvironment
    - FoodFoodProductionFacility
    range: SurfMaterialEnum
  indoor_surf:
    name: indoor_surf
    description: Type of indoor surface
    title: indoor surface
    examples:
    - value: wall
    from_schema: https://w3id.org/mixs
    keywords:
    - indoor
    - surface
    slot_uri: MIXS:0000764
    alias: indoor_surf
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - BuiltEnvironment
    - FoodFoodProductionFacility
    range: IndoorSurfEnum
  avg_occup:
    name: avg_occup
    description: Daily average occupancy of room. Indicate the number of person(s)
      daily occupying the sampling room
    title: average daily occupancy
    examples:
    - value: '6'
    from_schema: https://w3id.org/mixs
    keywords:
    - average
    slot_uri: MIXS:0000775
    alias: avg_occup
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - BuiltEnvironment
    - FoodFoodProductionFacility
    range: float
  samp_floor:
    name: samp_floor
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration
    description: The floor of the building, where the sampling room is located
    title: sampling floor
    examples:
    - value: 4th floor
    from_schema: https://w3id.org/mixs
    keywords:
    - floor
    string_serialization: '[1st floor|2nd floor|{integer} floor|basement|lobby]'
    slot_uri: MIXS:0000828
    alias: samp_floor
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - BuiltEnvironment
    - FoodFoodProductionFacility
    range: string
  genetic_mod:
    name: genetic_mod
    annotations:
      Expected_value:
        tag: Expected_value
        value: PMID, DOI, URL or text
    description: Genetic modifications of the genome of an organism, which may occur
      naturally by spontaneous mutation, or be introduced by some experimental means,
      e.g. specification of a transgene or the gene knocked-out or details of transient
      transfection
    title: genetic modification
    examples:
    - value: aox1A transgenic
    from_schema: https://w3id.org/mixs
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000859
    alias: genetic_mod
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - PlantAssociated
    range: string
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: 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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
  samp_type:
    name: samp_type
    description: The type of material from which the sample was obtained. For the
      Hydrocarbon package, samples include types like core, rock trimmings, drill
      cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid,
      produced water, injected water, swabs, etc. For the Food Package, samples are
      usually categorized as food, body products or tissues, or environmental material.
      This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246)
    title: sample type
    examples:
    - value: built environment sample [GENEPIO:0001248]
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - type
    slot_uri: MIXS:0000998
    alias: samp_type
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - 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
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: 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: MimarksSFoodFoodProductionFacility
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
    multivalued: true
  facility_type:
    name: facility_type
    description: Establishment details about the type of facility where the sample
      was taken. This is independent of the specific product(s) within the facility
    title: facility type
    examples:
    - value: manufacturing-processing
    from_schema: https://w3id.org/mixs
    keywords:
    - facility
    - type
    slot_uri: MIXS:0001252
    alias: facility_type
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFoodProductionFacility
    range: FacilityTypeEnum
    multivalued: true
  food_trav_mode:
    name: food_trav_mode
    description: A descriptor for the method of movement of food commodity along the
      food distribution system.  This field accepts terms listed under travel mode
      (http://purl.obolibrary.org/obo/GENEPIO_0001064). If the proper descrptor is
      not listed please use text to describe the mode of travel. Multiple terms can
      be separated by one or more pipes
    title: food shipping transportation method
    examples:
    - value: train travel [GENEPIO:0001060]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - method
    - transport
    slot_uri: MIXS:0001137
    alias: food_trav_mode
    owner: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: 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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  num_samp_collect:
    name: num_samp_collect
    description: The number of samples collected during the current sampling event
    title: number of samples collected
    examples:
    - value: 116 samples
    from_schema: https://w3id.org/mixs
    keywords:
    - number
    - sample
    slot_uri: MIXS:0001224
    alias: num_samp_collect
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - 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
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  hygienic_area:
    name: hygienic_area
    annotations:
      Expected_value:
        tag: Expected_value
        value: Expected value
    description: The subdivision of areas within a food production facility according
      to hygienic requirements. This field accepts terms listed under hygienic food
      production area (http://purl.obolibrary.org/obo/ENVO). Please add a term that
      most accurately indicates the hygienic area your sample was taken from according
      to the definitions provided
    title: hygienic food production area
    examples:
    - value: Low Hygiene Area
    from_schema: https://w3id.org/mixs
    keywords:
    - area
    - food
    - production
    slot_uri: MIXS:0001253
    alias: hygienic_area
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFoodProductionFacility
    range: string
  env_monitoring_zone:
    name: env_monitoring_zone
    annotations:
      Expected_value:
        tag: Expected_value
        value: ENVO
    description: An environmental monitoring zone is a formal designation as part
      of an environmental monitoring program, in which areas of a food production
      facility are categorized, commonly as zones 1-4, based on likelihood or risk
      of foodborne pathogen contamination. This field accepts terms listed under food
      production environmental monitoring zone (http://purl.obolibrary.org/obo/ENVO).
      Please add a term to indicate the environmental monitoring zone the sample was
      taken from
    title: food production environmental monitoring zone
    examples:
    - value: Zone 1
    from_schema: https://w3id.org/mixs
    keywords:
    - environmental
    - food
    - production
    slot_uri: MIXS:0001254
    alias: env_monitoring_zone
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFoodProductionFacility
    range: string
  area_samp_size:
    name: area_samp_size
    annotations:
      Expected_value:
        tag: Expected_value
        value: measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: centimeter
    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
      sample collected
    title: area sampled size
    examples:
    - value: 12 centimeter x 12 centimeter
    from_schema: https://w3id.org/mixs
    keywords:
    - area
    - sample
    - size
    string_serialization: '{integer} {unit} x {integer} {unit}'
    slot_uri: MIXS:0001255
    alias: area_samp_size
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFoodProductionFacility
    range: string
  samp_surf_moisture:
    name: samp_surf_moisture
    description: Degree of water held on a sampled surface.  If present, user can
      state the degree of water held on surface (intermittent moisture, submerged).
      If no surface moisture is present indicate not present
    title: sample surface moisture
    examples:
    - value: submerged
    from_schema: https://w3id.org/mixs
    keywords:
    - moisture
    - sample
    - surface
    slot_uri: MIXS:0001256
    alias: samp_surf_moisture
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFoodProductionFacility
    range: SampSurfMoistureEnum
    multivalued: true
  samp_loc_condition:
    name: samp_loc_condition
    description: The condition of the sample location at the time of sampling
    title: sample location condition
    examples:
    - value: new
    from_schema: https://w3id.org/mixs
    keywords:
    - condition
    - location
    - sample
    slot_uri: MIXS:0001257
    alias: samp_loc_condition
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFoodProductionFacility
    range: SampLocConditionEnum
  biocide_used:
    name: biocide_used
    annotations:
      Expected_value:
        tag: Expected_value
        value: commercial name of biocide, active ingredient in biocide or class of
          biocide
    description: Substance intended for preventing, neutralizing, destroying, repelling,
      or mitigating the effects of any pest or microorganism; that inhibits the growth,
      reproduction, and activity of organisms, including fungal cells; decreases the
      number of fungi or pests present; deters microbial growth and degradation of
      other ingredients in the formulation. Indicate the biocide used on the location
      where the sample was taken. Multiple terms can be separated by pipes
    title: biocide
    examples:
    - value: Quaternary ammonium compound|SterBac
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0001258
    alias: biocide_used
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFoodProductionFacility
    range: string
    multivalued: true
  ster_meth_samp_room:
    name: ster_meth_samp_room
    annotations:
      Expected_value:
        tag: Expected_value
        value: ENVO:01001026
    description: The method used to sterilize the sampling room. This field accepts
      terms listed under electromagnetic radiation (http://purl.obolibrary.org/obo/ENVO_01001026).
      If the proper descriptor is not listed, please use text to describe the sampling
      room sterilization method. Multiple terms can be separated by pipes
    title: sampling room sterilization method
    examples:
    - value: ultraviolet radiation [ENVO:21001216]|infrared radiation [ENVO:21001214]
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    - room
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001259
    alias: ster_meth_samp_room
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    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
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - 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: MimarksSFoodFoodProductionFacility
    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
  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: MimarksSFoodFoodProductionFacility
    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
  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: MimarksSFoodFoodProductionFacility
    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
  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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    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
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - MimarksC
    - FoodFoodProductionFacility
    range: string
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  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: MimarksSFoodFoodProductionFacility
    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_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: MimarksSFoodFoodProductionFacility
    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_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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: SampTransportContEnum
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  nucl_acid_ext_kit:
    name: nucl_acid_ext_kit
    annotations:
      Expected_value:
        tag: Expected_value
        value: The name of an extraction kit
    description: The name of the extraction kit used to recover the nucleic acid fraction
      of an input material is performed
    title: nucleic acid extraction kit
    examples:
    - value: Qiagen PowerSoil Kit
    from_schema: https://w3id.org/mixs
    keywords:
    - kit
    slot_uri: MIXS:0001223
    alias: nucl_acid_ext_kit
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  library_prep_kit:
    name: library_prep_kit
    annotations:
      Expected_value:
        tag: Expected_value
        value: name of library preparation kit
    description: Packaged kits (containing adapters, indexes, enzymes, buffers etc.),
      tailored for specific sequencing workflows, which allow the simplified preparation
      of sequencing-ready libraries for small genomes, amplicons, and plasmids
    title: library preparation kit
    examples:
    - value: Illumina DNA Prep
    from_schema: https://w3id.org/mixs
    keywords:
    - kit
    - library
    - preparation
    slot_uri: MIXS:0001145
    alias: library_prep_kit
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  sequencing_kit:
    name: sequencing_kit
    annotations:
      Expected_value:
        tag: Expected_value
        value: name of sequencing kit used
    description: Pre-filled, ready-to-use reagent cartridges. Used to produce improved
      chemistry, cluster density and read length as well as improve quality (Q) scores.
      Reagent components are encoded to interact with the sequencing system to validate
      compatibility with user-defined applications. Indicate name of the sequencing
      kit
    title: sequencing kit
    examples:
    - value: NextSeq 500/550 High Output Kit v2.5 (75 Cycles)
    from_schema: https://w3id.org/mixs
    keywords:
    - kit
    slot_uri: MIXS:0001155
    alias: sequencing_kit
    owner: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  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: MimarksSFoodFoodProductionFacility
    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_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: MimarksSFoodFoodProductionFacility
    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_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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  food_source:
    name: food_source
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON term
    description: Type of plant or animal from which the food product or its major
      ingredient is derived or a chemical food source [FDA CFSAN 1995]
    title: food source
    examples:
    - value: giant tiger prawn [FOODON:03412612]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - source
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0001139
    alias: food_source
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    range: string
    multivalued: 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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    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_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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: 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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: 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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: FoodTraceListEnum
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  spec_intended_cons:
    name: spec_intended_cons
    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)
    title: specific intended consumer
    examples:
    - value: senior as food consumer [FOODON:03510254]
    from_schema: https://w3id.org/mixs
    keywords:
    - consumer
    slot_uri: MIXS:0001234
    alias: spec_intended_cons
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFoodProductionFacility
    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
  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: MimarksSFoodFoodProductionFacility
    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
  dietary_claim_use:
    name: dietary_claim_use
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03510023
    description: These descriptors are used either for foods intended for special
      dietary use as defined in 21 CFR 105 or for foods that have special characteristics
      indicated in the name or labeling. This field accepts terms listed under dietary
      claim or use (http://purl.obolibrary.org/obo/FOODON_03510023). Multiple terms
      can be separated by one or more pipes, but please consider limiting this list
      to the most prominent dietary claim or use
    title: dietary claim or use
    examples:
    - value: No preservatives [FOODON:03510113]
    from_schema: https://w3id.org/mixs
    keywords:
    - diet
    - use
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001199
    alias: dietary_claim_use
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  food_allergen_label:
    name: food_allergen_label
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03510213
    description: A label indication that the product contains a recognized allergen.
      This field accepts terms listed under dietary claim or use (http://purl.obolibrary.org/obo/FOODON_03510213)
    title: food allergen labeling
    examples:
    - value: food allergen labelling about crustaceans and products thereof [FOODON:03510215]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001201
    alias: food_allergen_label
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  food_prod_char:
    name: food_prod_char
    description: Descriptors of the food production system such as wild caught, free-range,
      organic, free-range, industrial, dairy, beef
    title: food production characteristics
    examples:
    - value: wild caught
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - production
    slot_uri: MIXS:0001136
    alias: food_prod_char
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    range: string
    multivalued: true
  prod_label_claims:
    name: prod_label_claims
    description: Labeling claims containing descriptors such as wild caught, free-range,
      organic, free-range, industrial, hormone-free, antibiotic free, cage free. Can
      include more than one term, separated by ";"
    title: production labeling claims
    examples:
    - value: free range
    from_schema: https://w3id.org/mixs
    keywords:
    - production
    slot_uri: MIXS:prod_label_claims
    alias: prod_label_claims
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    range: string
    multivalued: true
  food_name_status:
    name: food_name_status
    description: A datum indicating that use of a food product name is regulated in
      some legal jurisdiction. This field accepts terms listed under food product
      name legal status (http://purl.obolibrary.org/obo/FOODON_03530087)
    title: food product name legal status
    examples:
    - value: protected geographic indication [FOODON:03530256]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    - product
    - status
    slot_uri: MIXS:0001206
    alias: food_name_status
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - 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_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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - 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: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  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: MimarksSFoodFoodProductionFacility
    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_medium:
    name: food_pack_medium
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03480020
    description: The medium in which the food is packed for preservation and handling
      or the medium surrounding homemade foods, e.g., peaches cooked in sugar syrup.
      The packing medium may provide a controlled environment for the food. It may
      also serve to improve palatability and consumer appeal.  This includes edible
      packing media (e.g. fruit juice), gas other than air (e.g. carbon dioxide),
      vacuum packed, or packed with aerosol propellant. This field accepts terms under
      food packing medium (http://purl.obolibrary.org/obo/FOODON_03480020). Multiple
      terms may apply and can be separated by pipes
    title: food packing medium
    examples:
    - value: vacuum-packed [FOODON:03480027]
    from_schema: https://w3id.org/mixs
    keywords:
    - food
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001134
    alias: food_pack_medium
    owner: MimarksSFoodFoodProductionFacility
    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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: 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: MimarksSFoodFoodProductionFacility
    domain_of:
    - Agriculture
    - 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
  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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  repository_name:
    name: repository_name
    annotations:
      Expected_value:
        tag: Expected_value
        value: Institution
    description: The name of the institution where the sample or DNA extract is held
      or "sample not available" if the sample was used in its entirety for analysis
      or otherwise not retained
    title: repository name
    examples:
    - value: FDA CFSAN Microbiology Laboratories
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0001152
    alias: repository_name
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  intended_consumer:
    name: intended_consumer
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON_03510136 or NCBI taxid
    description: Food consumer type, human or animal, for which the food product is
      produced and marketed. This field accepts terms listed under food consumer group
      (http://purl.obolibrary.org/obo/FOODON_03510136) or NCBI taxid
    title: intended consumer
    examples:
    - value: 9606 o rsenior as food consumer [FOODON:03510254]
    from_schema: https://w3id.org/mixs
    keywords:
    - consumer
    string_serialization: '{integer}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001144
    alias: intended_consumer
    owner: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: 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: MimarksSFoodFoodProductionFacility
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
  misc_param:
    name: misc_param
    annotations:
      Expected_value:
        tag: Expected_value
        value: parameter name;measurement value
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    examples:
    - value: Bicarbonate ion concentration;2075 micromole per kilogram
    from_schema: https://w3id.org/mixs
    keywords:
    - parameter
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    alias: misc_param
    owner: MimarksSFoodFoodProductionFacility
    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:0010008_0016021