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Combination: MimagFoodAnimalAndAnimalFeed

MIxS data that complies with the Mimag checklist and the FoodAnimalAndAnimalFeed Extension

Inheritance

Terms

Name Cardinality and Range Description Inheritance
samp_name 1..1
String		 A local identifier or name that for the material sample used for extracting n... FoodAnimalAndAnimalFeed, Mimag
size_frac 0..1
String		 Filtering pore size used in sample preparation Mimag
lib_screen 0..1 recommended
String		 Specific enrichment or screening methods applied before and/or after creating... Mimag
ref_db 0..1
String		 List of database(s) used for ORF annotation, along with version number and re... Mimag
nucl_acid_amp 0..1 recommended
String		 A link to a literature reference, electronic resource or a standard operating... Mimag
lib_size 0..1 recommended
Integer		 Total number of clones in the library prepared for the project Mimag
contam_screen_input 0..1
CONTAMSCREENINPUTENUM		 The type of sequence data used as input Mimag
mid 0..1 recommended
String		 Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe... Mimag
assembly_name 0..1 recommended
String		 Name/version of the assembly provided by the submitter that is used in the ge... Mimag
temp 0..1 recommended
String		 Temperature of the sample at the time of sampling FoodAnimalAndAnimalFeed, Mimag
compl_score 1..1
String		 Completeness score is typically based on either the fraction of markers found... Mimag
trnas 0..1
String		 The total number of tRNAs identified from the SAG or MAG Mimag
mag_cov_software 0..1
MAGCOVSOFTWAREENUM		 Tool(s) used to determine the genome coverage if coverage is used as a binnin... Mimag
nucl_acid_ext 0..1 recommended
String		 A link to a literature reference, electronic resource or a standard operating... FoodAnimalAndAnimalFeed, Mimag
samp_size 0..1 recommended
String		 The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... FoodAnimalAndAnimalFeed, Mimag
alt 0..1 recommended
String		 Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... Mimag
bin_param 1..1
BINPARAMENUM		 The parameters that have been applied during the extraction of genomes from m... Mimag
bin_software 1..1
String		 Tool(s) used for the extraction of genomes from metagenomic datasets, where p... Mimag
source_mat_id 0..* recommended
String		 A unique identifier assigned to a material sample (as defined by http://rs Mimag
samp_vol_we_dna_ext 0..1
String		 Volume (ml) or mass (g) of total collected sample processed for DNA extractio... FoodAnimalAndAnimalFeed, Mimag
lib_reads_seqd 0..1 recommended
Integer		 Total number of clones sequenced from the library Mimag
rel_to_oxygen 0..1
RELTOOXYGENENUM		 Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ... Mimag
reassembly_bin 0..1
Boolean		 Has an assembly been performed on a genome bin extracted from a metagenomic a... Mimag
decontam_software 0..1
String		 Tool(s) used in contamination screening Mimag
samp_collect_device 0..1 recommended
String		 The device used to collect an environmental sample FoodAnimalAndAnimalFeed, Mimag
number_contig 0..1
Integer		 Total number of contigs in the cleaned/submitted assembly that makes up a giv... Mimag
trna_ext_software 0..1
String		 Tools used for tRNA identification Mimag
lib_layout 0..1 recommended
LIBLAYOUTENUM		 Specify whether to expect single, paired, or other configuration of reads Mimag
contam_screen_param 0..1
String		 Specific parameters used in the decontamination sofware, such as reference da... Mimag
assembly_qual 1..1
String		 The assembly quality category is based on sets of criteria outlined for each ... Mimag
ref_biomaterial 0..1
String		 Primary publication if isolated before genome publication; otherwise, primary... Mimag
project_name 1..1
String		 Name of the project within which the sequencing was organized FoodAnimalAndAnimalFeed, Mimag
lib_vector 0..1 recommended
String		 Cloning vector type(s) used in construction of libraries Mimag
adapters 0..1 recommended
String		 Adapters provide priming sequences for both amplification and sequencing of t... Mimag
neg_cont_type 0..1 recommended
NEGCONTTYPEENUM		 The substance or equipment used as a negative control in an investigation Mimag
assembly_software 1..1
String		 Tool(s) used for assembly, including version number and parameters Mimag
tax_ident 1..1
TAXIDENTENUM		 The phylogenetic marker(s) used to assign an organism name to the SAG or MAG Mimag
contam_score 1..1
Float		 The contamination score is based on the fraction of single-copy genes that ar... Mimag
annot 0..1
String		 Tool used for annotation, or for cases where annotation was provided by a com... Mimag
x16s_recover_software 0..1
String		 Tools used for 16S rRNA gene extraction Mimag
x16s_recover 0..1
Boolean		 Can a 16S gene be recovered from the submitted SAG or MAG? Mimag
pos_cont_type 0..1 recommended
String		 The substance, mixture, product, or apparatus used to verify that a process w... Mimag
feat_pred 0..1
String		 Method used to predict UViGs features such as ORFs, integration site, etc Mimag
compl_software 1..1
String		 Tools used for completion estimate, i Mimag
env_local_scale 1..1
String		 Report the entity or entities which are in the sample or specimen s local vic... Mimag
samp_mat_process 0..1 recommended
String		 A brief description of any processing applied to the sample during or after r... Mimag
sim_search_meth 0..1
String		 Tool used to compare ORFs with database, along with version and cutoffs used Mimag
depth 0..1 recommended
String		 The vertical distance below local surface Mimag
samp_collect_method 0..1 recommended
String		 The method employed for collecting the sample FoodAnimalAndAnimalFeed, Mimag
compl_appr 0..1
COMPLAPPRENUM		 The approach used to determine the completeness of a given genomic assembly, ... Mimag
env_medium 1..1
String		 Report the environmental material(s) immediately surrounding the sample or sp... Mimag
samp_taxon_id 1..1
String		 NCBI taxon id of the sample Mimag
geo_loc_name 1..1
String		 The geographical origin of the sample as defined by the country or sea name f... FoodAnimalAndAnimalFeed, Mimag
collection_date 1..1
Datetime		 The time of sampling, either as an instance (single point in time) or interva... FoodAnimalAndAnimalFeed, Mimag
seq_meth 1..1
String		 Sequencing machine used FoodAnimalAndAnimalFeed, Mimag
lat_lon 1..1
String		 The geographical origin of the sample as defined by latitude and longitude FoodAnimalAndAnimalFeed, Mimag
elev 0..1 recommended
String		 Elevation of the sampling site is its height above a fixed reference point, m... Mimag
env_broad_scale 1..1
String		 Report the major environmental system the sample or specimen came from Mimag
tax_class 0..1
String		 Method used for taxonomic classification, along with reference database used,... Mimag
experimental_factor 0..* recommended
String		 Variable aspects of an experiment design that can be used to describe an expe... FoodAnimalAndAnimalFeed, Mimag
associated_resource 0..* recommended
String		 A related resource that is referenced, cited, or otherwise associated to the ... Mimag
sop 0..* recommended
String		 Standard operating procedures used in assembly and/or annotation of genomes, ... Mimag
organism_count 0..*
String		 Total cell count of any organism (or group of organisms) per gram, volume or ... FoodAnimalAndAnimalFeed
spikein_count 0..1
String		 Total cell count of any organism (or group of organisms) per gram, volume or ... FoodAnimalAndAnimalFeed
samp_store_temp 0..1
String		 Temperature at which sample was stored, e FoodAnimalAndAnimalFeed
samp_store_dur 0..1
String		 Duration for which the sample was stored FoodAnimalAndAnimalFeed
pool_dna_extracts 0..1
String		 Indicate whether multiple DNA extractions were mixed FoodAnimalAndAnimalFeed
samp_store_loc 0..1
String		 Location at which sample was stored, usually name of a specific freezer/room FoodAnimalAndAnimalFeed
samp_transport_cont 0..1
SAMPTRANSPORTCONTENUM		 Conatiner in which the sample was stored during transport FoodAnimalAndAnimalFeed
perturbation 0..*
String		 Type of perturbation, e FoodAnimalAndAnimalFeed
coll_site_geo_feat 1..1
String		 Text or terms that describe the geographic feature where the food sample was ... FoodAnimalAndAnimalFeed
food_origin 1..1
String		 A reference to a place on the Earth, by its name or by its geographical locat... FoodAnimalAndAnimalFeed
food_prod 1..*
String		 Descriptors of the food production system or of the agricultural environment ... FoodAnimalAndAnimalFeed
food_product_type 1..1
String		 A food product type is a class of food products that is differentiated by its... FoodAnimalAndAnimalFeed
food_source 0..1
String		 Type of plant or animal from which the food product or its major ingredient i... FoodAnimalAndAnimalFeed
IFSAC_category 1..*
String		 The IFSAC food categorization scheme has five distinct levels to which foods ... FoodAnimalAndAnimalFeed
intended_consumer 1..*
String		 Food consumer type, human or animal, for which the food product is produced a... FoodAnimalAndAnimalFeed
samp_purpose 1..1
String		 The reason that the sample was collected FoodAnimalAndAnimalFeed
animal_am 0..1
String		 The name(s) (generic or brand) of the antimicrobial(s) given to the food anim... FoodAnimalAndAnimalFeed
animal_am_dur 0..1
String		 The duration of time (days) that the antimicrobial was administered to the fo... FoodAnimalAndAnimalFeed
animal_am_freq 0..1
Float		 The frequency per day that the antimicrobial was adminstered to the food anim... FoodAnimalAndAnimalFeed
animal_am_route 0..1
String		 The route by which the antimicrobial is adminstered into the body of the food... FoodAnimalAndAnimalFeed
animal_am_use 0..1
String		 The prescribed intended use of or the condition treated by the antimicrobial ... FoodAnimalAndAnimalFeed
animal_body_cond 0..1
ANIMALBODYCONDENUM		 Body condition scoring is a production management tool used to evaluate overa... FoodAnimalAndAnimalFeed
animal_diet 0..*
String		 If the isolate is from a food animal, the type of diet eaten by the food anim... FoodAnimalAndAnimalFeed
animal_feed_equip 0..*
String		 Description of the feeding equipment used for livestock FoodAnimalAndAnimalFeed
animal_group_size 0..1
Integer		 The number of food animals of the same species that are maintained together a... FoodAnimalAndAnimalFeed
animal_housing 0..*
String		 Description of the housing system of the livestock FoodAnimalAndAnimalFeed
animal_sex 0..1
ANIMALSEXENUM		 The sex and reproductive status of the food animal FoodAnimalAndAnimalFeed
bacterial_density 0..1
String		 Number of bacteria in sample, as defined by bacteria density (http://purl FoodAnimalAndAnimalFeed
cons_food_stor_dur 0..1
String		 The storage duration of the food commodity by the consumer, prior to onset of... FoodAnimalAndAnimalFeed
cons_food_stor_temp 0..1
String		 Temperature at which food commodity was stored by the consumer, prior to onse... FoodAnimalAndAnimalFeed
cons_purch_date 0..1
Datetime		 The date a food product was purchased by consumer FoodAnimalAndAnimalFeed
cons_qty_purchased 0..1
String		 The quantity of food purchased by consumer FoodAnimalAndAnimalFeed
cult_isol_date 0..1
Datetime		 The datetime marking the end of a process in which a sample yields a positive... FoodAnimalAndAnimalFeed
cult_result 0..1
CULTRESULTENUM		 Any result of a bacterial culture experiment reported as a binary assessment ... FoodAnimalAndAnimalFeed
cult_result_org 0..*
String		 Taxonomic information about the cultured organism(s) FoodAnimalAndAnimalFeed
cult_target 0..*
String		 The target microbial analyte in terms of investigation scope FoodAnimalAndAnimalFeed
enrichment_protocol 0..1
String		 The microbiological workflow or protocol followed to test for the presence or... FoodAnimalAndAnimalFeed
food_additive 0..*
String		 A substance or substances added to food to maintain or improve safety and fre... FoodAnimalAndAnimalFeed
food_contact_surf 0..*
String		 The specific container or coating materials in direct contact with the food FoodAnimalAndAnimalFeed
food_contain_wrap 0..1
String		 Type of container or wrapping defined by the main container material, the con... FoodAnimalAndAnimalFeed
food_cooking_proc 0..*
String		 The transformation of raw food by the application of heat FoodAnimalAndAnimalFeed
food_dis_point 0..*
String		 A reference to a place on the Earth, by its name or by its geographical locat... FoodAnimalAndAnimalFeed
food_dis_point_city 0..*
String		 A reference to a place on the Earth, by its name or by its geographical locat... FoodAnimalAndAnimalFeed
food_ingredient 0..*
String		 In this field, please list individual ingredients for multi-component food [F... FoodAnimalAndAnimalFeed
food_pack_capacity 0..1
String		 The maximum number of product units within a package FoodAnimalAndAnimalFeed
food_pack_integrity 0..*
String		 A term label and term id to describe the state of the packing material and te... FoodAnimalAndAnimalFeed
food_pack_medium 0..*
String		 The medium in which the food is packed for preservation and handling or the m... FoodAnimalAndAnimalFeed
food_preserv_proc 0..*
String		 The methods contributing to the prevention or retardation of microbial, enzym... FoodAnimalAndAnimalFeed
food_prior_contact 0..*
String		 The material the food contacted (e FoodAnimalAndAnimalFeed
food_prod_synonym 0..*
String		 Other names by which the food product is known by (e FoodAnimalAndAnimalFeed
food_product_qual 0..1
String		 Descriptors for describing food visually or via other senses, which is useful... FoodAnimalAndAnimalFeed
food_quality_date 0..1
String		 The date recommended for the use of the product while at peak quality, this d... FoodAnimalAndAnimalFeed
food_source_age 0..1
String		 The age of the food source host organim FoodAnimalAndAnimalFeed
food_trace_list 0..1
FOODTRACELISTENUM		 The FDA is proposing to establish additional traceability recordkeeping requi... FoodAnimalAndAnimalFeed
food_trav_mode 0..*
String		 A descriptor for the method of movement of food commodity along the food dist... FoodAnimalAndAnimalFeed
food_trav_vehic 0..*
String		 A descriptor for the mobile machine which is used to transport food commoditi... FoodAnimalAndAnimalFeed
food_treat_proc 0..*
String		 Used to specifically characterize a food product based on the treatment or pr... FoodAnimalAndAnimalFeed
HACCP_term 0..*
String		 Hazard Analysis Critical Control Points (HACCP) food safety terms; This field... FoodAnimalAndAnimalFeed
library_prep_kit 0..1
String		 Packaged kits (containing adapters, indexes, enzymes, buffers etc FoodAnimalAndAnimalFeed
lot_number 0..*
String		 A distinctive alpha-numeric identification code assigned by the manufacturer ... FoodAnimalAndAnimalFeed
microb_cult_med 0..1
String		 A culture medium used to select for, grow, and maintain prokaryotic microorga... FoodAnimalAndAnimalFeed
part_plant_animal 0..*
String		 The anatomical part of the organism being involved in food production or cons... FoodAnimalAndAnimalFeed
repository_name 0..*
String		 The name of the institution where the sample or DNA extract is held or "sampl... FoodAnimalAndAnimalFeed
samp_pooling 0..*
String		 Physical combination of several instances of like material, e FoodAnimalAndAnimalFeed
samp_rep_biol 0..1
String		 Measurements of biologically distinct samples that show biological variation FoodAnimalAndAnimalFeed
samp_rep_tech 0..1
String		 Repeated measurements of the same sample that show independent measures of th... FoodAnimalAndAnimalFeed
samp_source_mat_cat 0..1
String		 This is the scientific role or category that the subject organism or material... FoodAnimalAndAnimalFeed
samp_stor_device 0..1
String		 The container used to store the sample FoodAnimalAndAnimalFeed
samp_stor_media 0..1
String		 The liquid that is added to the sample collection device prior to sampling FoodAnimalAndAnimalFeed
samp_transport_dur 0..1
String		 The duration of time from when the sample was collected until processed FoodAnimalAndAnimalFeed
samp_transport_temp 0..1
String		 Temperature at which sample was transported, e FoodAnimalAndAnimalFeed
sequencing_kit 0..1
String		 Pre-filled, ready-to-use reagent cartridges FoodAnimalAndAnimalFeed
sequencing_location 0..1
String		 The location the sequencing run was performed FoodAnimalAndAnimalFeed
serovar_or_serotype 0..*
String		 A characterization of a cell or microorganism based on the antigenic properti... FoodAnimalAndAnimalFeed
spikein_AMR 0..*
String		 Qualitative description of a microbial response to antimicrobial agents FoodAnimalAndAnimalFeed
spikein_antibiotic 0..*
String		 Antimicrobials used in research study to assess effects of exposure on microb... FoodAnimalAndAnimalFeed
spikein_growth_med 0..*
String		 A liquid or gel containing nutrients, salts, and other factors formulated to ... FoodAnimalAndAnimalFeed
spikein_metal 0..*
String		 Heavy metals used in research study to assess effects of exposure on microbio... FoodAnimalAndAnimalFeed
spikein_org 0..*
String		 Taxonomic information about the spike-in organism(s) FoodAnimalAndAnimalFeed
spikein_serovar 0..*
String		 Taxonomic information about the spike-in organism(s) at the serovar or seroty... FoodAnimalAndAnimalFeed
spikein_strain 0..*
String		 Taxonomic information about the spike-in organism(s) at the strain level FoodAnimalAndAnimalFeed
study_design 0..*
String		 A plan specification comprised of protocols (which may specify how and what k... FoodAnimalAndAnimalFeed
study_inc_dur 0..1
String		 Sample incubation duration if unpublished or unvalidated method is used FoodAnimalAndAnimalFeed
study_inc_temp 0..1
String		 Sample incubation temperature if unpublished or unvalidated method is used FoodAnimalAndAnimalFeed
study_timecourse 0..1
String		 For time-course research studies involving samples of the food commodity, ind... FoodAnimalAndAnimalFeed
study_tmnt 0..*
String		 A process in which the act is intended to modify or alter some other material... FoodAnimalAndAnimalFeed
timepoint 0..1
String		 Time point at which a sample or observation is made or taken from a biomateri... FoodAnimalAndAnimalFeed
misc_param 0..*
String		 Any other measurement performed or parameter collected, that is not listed he... FoodAnimalAndAnimalFeed

Identifier and Mapping Information

Schema Source

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

LinkML Source

Direct

name: MimagFoodAnimalAndAnimalFeed
description: MIxS data that complies with the Mimag checklist and the FoodAnimalAndAnimalFeed
  Extension
title: Mimag combined with FoodAnimalAndAnimalFeed
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: FoodAnimalAndAnimalFeed
mixins:
- Mimag
class_uri: MIXS:0010011_0016019

Induced

name: MimagFoodAnimalAndAnimalFeed
description: MIxS data that complies with the Mimag checklist and the FoodAnimalAndAnimalFeed
  Extension
title: Mimag combined with FoodAnimalAndAnimalFeed
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: FoodAnimalAndAnimalFeed
mixins:
- Mimag
attributes:
  samp_name:
    name: samp_name
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ''
    description: A local identifier or name that for the material sample used for
      extracting nucleic acids, and subsequent sequencing. It can refer either to
      the original material collected or to any derived sub-samples. It can have any
      format, but we suggest that you make it concise, unique and consistent within
      your lab, and as informative as possible. INSDC requires every sample name from
      a single Submitter to be unique. Use of a globally unique identifier for the
      field source_mat_id is recommended in addition to sample_name
    title: sample name
    examples:
    - value: ISDsoil1
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - sample
    slot_uri: MIXS:0001107
    multivalued: false
    alias: samp_name
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: true
  size_frac:
    name: size_frac
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    multivalued: false
    alias: size_frac
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  lib_screen:
    name: lib_screen
    description: Specific enrichment or screening methods applied before and/or after
      creating libraries
    title: library screening strategy
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000043
    multivalued: false
    alias: lib_screen
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  ref_db:
    name: ref_db
    description: List of database(s) used for ORF annotation, along with version number
      and reference to website or publication
    title: reference database(s)
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{database};{version};{reference}'
    slot_uri: MIXS:0000062
    multivalued: false
    alias: ref_db
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  nucl_acid_amp:
    name: nucl_acid_amp
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the enzymatic amplification (PCR,
      TMA, NASBA) of specific nucleic acids
    title: nucleic acid amplification
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000038
    multivalued: false
    alias: nucl_acid_amp
    owner: MimagFoodAnimalAndAnimalFeed
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000039
    multivalued: false
    alias: lib_size
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    recommended: true
  contam_screen_input:
    name: contam_screen_input
    description: The type of sequence data used as input
    title: contamination screening input
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000005
    multivalued: false
    alias: contam_screen_input
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - Misag
    range: CONTAM_SCREEN_INPUT_ENUM
    required: false
    recommended: false
  mid:
    name: mid
    description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
      used to specifically tag unique samples in a sequencing run. Sequence should
      be reported in uppercase letters
    title: multiplex identifiers
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000047
    multivalued: false
    alias: mid
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^[ACGTRKSYMWBHDVN]+$
    structured_pattern:
      syntax: ^{ambiguous_nucleotides}$
      interpolated: true
      partial_match: true
  assembly_name:
    name: assembly_name
    description: Name/version of the assembly provided by the submitter that is used
      in the genome browsers and in the community
    title: assembly name
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text} {text}'
    slot_uri: MIXS:0000057
    multivalued: false
    alias: assembly_name
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  temp:
    name: temp
    description: Temperature of the sample at the time of sampling
    title: temperature
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000113
    multivalued: false
    alias: temp
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  compl_score:
    name: compl_score
    description: 'Completeness score is typically based on either the fraction of
      markers found as compared to a database or the percent of a genome found as
      compared to a closely related reference genome. High Quality Draft: >90%, Medium
      Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated
      completeness scores'
    title: completeness score
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '[high|med|low];{percentage}'
    slot_uri: MIXS:0000069
    multivalued: false
    alias: compl_score
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: string
    required: true
  trnas:
    name: trnas
    description: The total number of tRNAs identified from the SAG or MAG
    title: number of standard tRNAs extracted
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{integer}'
    slot_uri: MIXS:0000067
    multivalued: false
    alias: trnas
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  mag_cov_software:
    name: mag_cov_software
    description: Tool(s) used to determine the genome coverage if coverage is used
      as a binning parameter in the extraction of genomes from metagenomic datasets
    title: MAG coverage software
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000080
    multivalued: false
    alias: mag_cov_software
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - Miuvig
    range: MAG_COV_SOFTWARE_ENUM
    required: false
    recommended: false
  nucl_acid_ext:
    name: nucl_acid_ext
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the material separation to recover
      the nucleic acid fraction from a sample
    title: nucleic acid extraction
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000037
    multivalued: false
    alias: nucl_acid_ext
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000001
    multivalued: false
    alias: samp_size
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  alt:
    name: alt
    description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric
      balloons and heights of places such as atmospheric layers and clouds. It is
      used to measure the height of an object which is above the earth's surface.
      In this context, the altitude measurement is the vertical distance between the
      earth's surface above sea level and the sampled position in the air
    title: altitude
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000094
    multivalued: false
    alias: alt
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - HostAssociated
    - MiscellaneousNaturalOrArtificialEnvironment
    - SymbiontAssociated
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  bin_param:
    name: bin_param
    description: The parameters that have been applied during the extraction of genomes
      from metagenomic datasets
    title: binning parameters
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000077
    alias: bin_param
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - Miuvig
    range: BIN_PARAM_ENUM
    required: true
  bin_software:
    name: bin_software
    description: Tool(s) used for the extraction of genomes from metagenomic datasets,
      where possible include a product ID (PID) of the tool(s) used
    title: binning software
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{software};{version}{PID}'
    slot_uri: MIXS:0000078
    multivalued: false
    alias: bin_software
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - Miuvig
    range: string
    required: true
  source_mat_id:
    name: source_mat_id
    description: A unique identifier assigned to a material sample (as defined by
      http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
      digital record of a material sample) used for extracting nucleic acids, and
      subsequent sequencing. The identifier can refer either to the original material
      collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
      /bio_material, or /culture_collection may or may not share the same value as
      the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
      may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
      sampled tissue with the same identifier. However, the /culture_collection qualifier
      may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
      would refer to an identifier from some derived culture from which the nucleic
      acids were extracted (e.g. xatc123 or ark:/2154/R2)
    title: source material identifiers
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000026
    multivalued: true
    alias: source_mat_id
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - SymbiontAssociated
    range: string
    recommended: true
  samp_vol_we_dna_ext:
    name: samp_vol_we_dna_ext
    description: 'Volume (ml) or mass (g) of total collected sample processed for
      DNA extraction. Note: total sample collected should be entered under the term
      Sample Size (MIXS:0000001)'
    title: sample volume or weight for DNA extraction
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000111
    multivalued: false
    alias: samp_vol_we_dna_ext
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  lib_reads_seqd:
    name: lib_reads_seqd
    description: Total number of clones sequenced from the library
    title: library reads sequenced
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000040
    multivalued: false
    alias: lib_reads_seqd
    owner: MimagFoodAnimalAndAnimalFeed
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000015
    multivalued: false
    alias: rel_to_oxygen
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    range: REL_TO_OXYGEN_ENUM
    required: false
    recommended: false
  reassembly_bin:
    name: reassembly_bin
    description: Has an assembly been performed on a genome bin extracted from a metagenomic
      assembly?
    title: reassembly post binning
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000079
    multivalued: false
    alias: reassembly_bin
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - Miuvig
    range: boolean
    required: false
    recommended: false
  decontam_software:
    name: decontam_software
    description: Tool(s) used in contamination screening
    title: decontamination software
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '[checkm/refinem|anvi''o|prodege|bbtools:decontaminate.sh|acdc|combination]'
    slot_uri: MIXS:0000074
    multivalued: false
    alias: decontam_software
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - Misag
    range: string
    required: false
    recommended: false
  samp_collect_device:
    name: samp_collect_device
    description: The device used to collect an environmental sample. This field accepts
      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
    title: sample collection device
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000002
    multivalued: false
    alias: samp_collect_device
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: true
  number_contig:
    name: number_contig
    description: Total number of contigs in the cleaned/submitted assembly that makes
      up a given genome, SAG, MAG, or UViG
    title: number of contigs
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000060
    multivalued: false
    alias: number_contig
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: integer
    required: false
    recommended: false
  trna_ext_software:
    name: trna_ext_software
    description: Tools used for tRNA identification
    title: tRNA extraction software
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000068
    multivalued: false
    alias: trna_ext_software
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  lib_layout:
    name: lib_layout
    description: Specify whether to expect single, paired, or other configuration
      of reads
    title: library layout
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000041
    multivalued: false
    alias: lib_layout
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: LIB_LAYOUT_ENUM
    recommended: true
  contam_screen_param:
    name: contam_screen_param
    description: Specific parameters used in the decontamination sofware, such as
      reference database, coverage, and kmers. Combinations of these parameters may
      also be used, i.e. kmer and coverage, or reference database and kmer
    title: contamination screening parameters
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '[ref db|kmer|coverage|combination];{text|integer}'
    slot_uri: MIXS:0000073
    multivalued: false
    alias: contam_screen_param
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - Misag
    range: string
    required: false
    recommended: false
  assembly_qual:
    name: assembly_qual
    description: 'The assembly quality category is based on sets of criteria outlined
      for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
      contiguous sequence per replicon without gaps or ambiguities with a consensus
      error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
      where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes
      and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no
      review of assembly other than reporting of standard assembly statistics. Low
      Quality Draft:Many fragments with little to no review of assembly other than
      reporting of standard assembly statistics. Assembly statistics include, but
      are not limited to total assembly size, number of contigs, contig N50/L50, and
      maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence
      per replicon without gaps or ambiguities, with extensive manual review and editing
      to annotate putative gene functions and transcriptional units. High-quality
      draft genome: One or multiple fragments, totaling   90% of the expected genome
      or replicon sequence or predicted complete. Genome fragment(s): One or multiple
      fragments, totalling < 90% of the expected genome or replicon sequence, or for
      which no genome size could be estimated'
    title: assembly quality
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '[Finished genome|High-quality draft genome|Medium-quality
      draft genome|Low-quality draft genome|Genome fragment(s)]'
    slot_uri: MIXS:0000056
    multivalued: false
    alias: assembly_qual
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    required: true
  ref_biomaterial:
    name: ref_biomaterial
    description: Primary publication if isolated before genome publication; otherwise,
      primary genome report
    title: reference for biomaterial
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000025
    multivalued: false
    alias: ref_biomaterial
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  project_name:
    name: project_name
    description: Name of the project within which the sequencing was organized
    title: project name
    examples:
    - value: Forest soil metagenome
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - project
    slot_uri: MIXS:0000092
    multivalued: false
    alias: project_name
    owner: MimagFoodAnimalAndAnimalFeed
    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
    description: Cloning vector type(s) used in construction of libraries
    title: library vector
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000042
    multivalued: false
    alias: lib_vector
    owner: MimagFoodAnimalAndAnimalFeed
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{dna};{dna}'
    slot_uri: MIXS:0000048
    multivalued: false
    alias: adapters
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  neg_cont_type:
    name: neg_cont_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration or text
    description: The substance or equipment used as a negative control in an investigation
    title: negative control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - type
    slot_uri: MIXS:0001321
    multivalued: false
    alias: neg_cont_type
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: NEG_CONT_TYPE_ENUM
    recommended: true
  assembly_software:
    name: assembly_software
    description: Tool(s) used for assembly, including version number and parameters
    title: assembly software
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000058
    multivalued: false
    alias: assembly_software
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  tax_ident:
    name: tax_ident
    description: The phylogenetic marker(s) used to assign an organism name to the
      SAG or MAG
    title: taxonomic identity marker
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000053
    alias: tax_ident
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: TAX_IDENT_ENUM
    required: true
  contam_score:
    name: contam_score
    description: 'The contamination score is based on the fraction of single-copy
      genes that are observed more than once in a query genome. The following scores
      are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low
      Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be
      deposited into any of the public databases'
    title: contamination score
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000072
    multivalued: false
    alias: contam_score
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - Misag
    range: float
    required: true
  annot:
    name: annot
    description: Tool used for annotation, or for cases where annotation was provided
      by a community jamboree or model organism database rather than by a specific
      submitter
    title: annotation
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000059
    multivalued: false
    alias: annot
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    required: false
    recommended: false
  x16s_recover_software:
    name: x16s_recover_software
    description: Tools used for 16S rRNA gene extraction
    title: 16S recovery software
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000066
    multivalued: false
    alias: x16s_recover_software
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - Misag
    range: string
    required: false
    recommended: false
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  x16s_recover:
    name: x16s_recover
    description: Can a 16S gene be recovered from the submitted SAG or MAG?
    title: 16S recovered
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000065
    multivalued: false
    alias: x16s_recover
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - Misag
    range: boolean
    required: false
    recommended: false
  pos_cont_type:
    name: pos_cont_type
    description: The substance, mixture, product, or apparatus used to verify that
      a process which is part of an investigation delivers a true positive
    title: positive control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - type
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    multivalued: false
    alias: pos_cont_type
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    recommended: true
  feat_pred:
    name: feat_pred
    description: Method used to predict UViGs features such as ORFs, integration site,
      etc
    title: feature prediction
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000061
    multivalued: false
    alias: feat_pred
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  compl_software:
    name: compl_software
    description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
    title: completeness software
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{software};{version}'
    slot_uri: MIXS:0000070
    multivalued: false
    alias: compl_software
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: string
    required: true
  env_local_scale:
    name: env_local_scale
    annotations:
      Expected_value:
        tag: Expected_value
        value: Environmental entities having causal influences upon the entity at
          time of sampling
    description: 'Report the entity or entities which are in the sample or specimen
      s local vicinity and which you believe have significant causal influences on
      your sample or specimen. We recommend using EnvO terms which are of smaller
      spatial grain than your entry for env_broad_scale. Terms, such as anatomical
      sites, from other OBO Library ontologies which interoperate with EnvO (e.g.
      UBERON) are accepted in this field. EnvO documentation about how to use the
      field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: local environmental context
    examples:
    - value: hillside [ENVO:01000333]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - context
    - environmental
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000013
    multivalued: false
    alias: env_local_scale
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
  samp_mat_process:
    name: samp_mat_process
    description: A brief description of any processing applied to the sample during
      or after retrieving the sample from environment, or a link to the relevant protocol(s)
      performed
    title: sample material processing
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000016
    multivalued: false
    alias: samp_mat_process
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  sim_search_meth:
    name: sim_search_meth
    description: Tool used to compare ORFs with database, along with version and cutoffs
      used
    title: similarity search method
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000063
    multivalued: false
    alias: sim_search_meth
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  depth:
    name: depth
    description: The vertical distance below local surface. For sediment or soil samples
      depth is measured from sediment or soil surface, respectively. Depth can be
      reported as an interval for subsurface samples
    title: depth
    examples:
    - value: 10 meter
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000018
    multivalued: false
    alias: depth
    owner: MimagFoodAnimalAndAnimalFeed
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0001225
    multivalued: false
    alias: samp_collect_method
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: true
  compl_appr:
    name: compl_appr
    description: The approach used to determine the completeness of a given genomic
      assembly, which would typically make use of a set of conserved marker genes
      or a closely related reference genome. For UViG completeness, include reference
      genome or group used, and contig feature suggesting a complete genome
    title: completeness approach
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000071
    alias: compl_appr
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Mimag
    - Misag
    - Miuvig
    range: COMPL_APPR_ENUM
    required: false
    recommended: false
  env_medium:
    name: env_medium
    description: 'Report the environmental material(s) immediately surrounding the
      sample or specimen at the time of sampling. We recommend using subclasses of
      ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
      documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
      . Terms from other OBO ontologies are permissible as long as they reference
      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
      (e.g. a tree, a leaf, a table top)'
    title: environmental medium
    examples:
    - value: bluegrass field soil [ENVO:00005789]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - environmental
    slot_uri: MIXS:0000014
    multivalued: false
    alias: env_medium
    owner: MimagFoodAnimalAndAnimalFeed
    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-6-2-rc
    keywords:
    - dna
    - identifier
    - sample
    - taxon
    slot_uri: MIXS:0001320
    multivalued: false
    alias: samp_taxon_id
    owner: MimagFoodAnimalAndAnimalFeed
    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-6-2-rc
    keywords:
    - geographic
    - location
    slot_uri: MIXS:0000010
    multivalued: false
    alias: geo_loc_name
    owner: MimagFoodAnimalAndAnimalFeed
    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-6-2-rc
    keywords:
    - date
    slot_uri: MIXS:0000011
    multivalued: false
    alias: collection_date
    owner: MimagFoodAnimalAndAnimalFeed
    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-6-2-rc
    keywords:
    - method
    slot_uri: MIXS:0000050
    multivalued: false
    alias: seq_meth
    owner: MimagFoodAnimalAndAnimalFeed
    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
    annotations:
      Expected_value:
        tag: Expected_value
        value: decimal degrees,  limit to 8 decimal points
    description: The geographical origin of the sample as defined by latitude and
      longitude. The values should be reported in decimal degrees and in WGS84 system
    title: geographic location (latitude and longitude)
    examples:
    - value: 50.586825 6.408977
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - geographic
    - location
    string_serialization: '{float} {float}'
    slot_uri: MIXS:0000009
    alias: lat_lon
    owner: MimagFoodAnimalAndAnimalFeed
    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
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit
    title: elevation
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000093
    multivalued: false
    alias: elev
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - HostAssociated
    - HydrocarbonResourcesCores
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - Water
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  env_broad_scale:
    name: env_broad_scale
    description: 'Report the major environmental system the sample or specimen came
      from. The system(s) identified should have a coarse spatial grain, to provide
      the general environmental context of where the sampling was done (e.g. in the
      desert or a rainforest). We recommend using subclasses of EnvO s biome class:  http://purl.obolibrary.org/obo/ENVO_00000428.
      EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: broad-scale environmental context
    examples:
    - value: rangeland biome [ENVO:01000247]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - context
    - environmental
    slot_uri: MIXS:0000012
    multivalued: false
    alias: env_broad_scale
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  tax_class:
    name: tax_class
    description: Method used for taxonomic classification, along with reference database
      used, classification rank, and thresholds used to classify new genomes
    title: taxonomic classification
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000064
    multivalued: false
    alias: tax_class
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  experimental_factor:
    name: experimental_factor
    description: Variable aspects of an experiment design that can be used to describe
      an experiment, or set of experiments, in an increasingly detailed manner. This
      field accepts ontology terms from Experimental Factor Ontology (EFO) and/or
      Ontology for Biomedical Investigations (OBI)
    title: experimental factor
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000008
    multivalued: true
    alias: experimental_factor
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: true
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  associated_resource:
    name: associated_resource
    annotations:
      Expected_value:
        tag: Expected_value
        value: reference to resource
    description: A related resource that is referenced, cited, or otherwise associated
      to the sequence
    title: relevant electronic resources
    examples:
    - value: http://www.earthmicrobiome.org/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - resource
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000091
    multivalued: true
    alias: associated_resource
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  sop:
    name: sop
    description: Standard operating procedures used in assembly and/or annotation
      of genomes, metagenomes or environmental sequences
    title: relevant standard operating procedures
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000090
    multivalued: true
    alias: sop
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  organism_count:
    name: organism_count
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
    slot_uri: MIXS:0000103
    multivalued: true
    alias: organism_count
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  spikein_count:
    name: spikein_count
    annotations:
      Expected_value:
        tag: Expected_value
        value: organism name;measurement value;enumeration
      Preferred_unit:
        tag: Preferred_unit
        value: colony forming units per milliliter; colony forming units per gram
          of dry weight
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) should
      also be provided (example: total prokaryotes; 3.5e7 cells per ml; qPCR)'
    title: spike-in organism count
    examples:
    - value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - count
    - organism
    - spike
    string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
    slot_uri: MIXS:0001335
    multivalued: false
    alias: spikein_count
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  samp_store_temp:
    name: samp_store_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature at which sample was stored, e.g. -80 degree Celsius
    title: sample storage temperature
    examples:
    - value: -80 degree Celsius
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - sample
    - storage
    - temperature
    slot_uri: MIXS:0000110
    multivalued: false
    alias: samp_store_temp
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_store_dur:
    name: samp_store_dur
    description: Duration for which the sample was stored. Indicate the duration for
      which the sample was stored written in ISO 8601 format
    title: sample storage duration
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000116
    multivalued: false
    alias: samp_store_dur
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
    structured_pattern:
      syntax: ^{duration}$
      interpolated: true
      partial_match: true
  pool_dna_extracts:
    name: pool_dna_extracts
    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)
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{boolean},{integer}'
    slot_uri: MIXS:0000325
    multivalued: false
    alias: pool_dna_extracts
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - Soil
    range: string
    required: false
    recommended: false
  samp_store_loc:
    name: samp_store_loc
    description: Location at which sample was stored, usually name of a specific freezer/room
    title: sample storage location
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000755
    multivalued: false
    alias: samp_store_loc
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  samp_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-6-2-rc
    keywords:
    - sample
    - transport
    slot_uri: MIXS:0001230
    multivalued: false
    alias: samp_transport_cont
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: SAMP_TRANSPORT_CONT_ENUM
    required: false
    recommended: false
  perturbation:
    name: perturbation
    description: Type of perturbation, e.g. chemical administration, physical disturbance,
      etc., coupled with perturbation regimen including how many times the perturbation
      was repeated, how long each perturbation lasted, and the start and end time
      of the entire perturbation period; can include multiple perturbation types
    title: perturbation
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000754
    multivalued: true
    alias: perturbation
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - feature
    - geographic
    - site
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001183
    multivalued: false
    alias: coll_site_geo_feat
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
  food_origin:
    name: food_origin
    description: A reference to a place on the Earth, by its name or by its geographical
      location that describes the origin of the food commodity, either in terms of
      its cultivation or production. This field accepts terms listed under geographic
      location (http://purl.obolibrary.org/obo/GAZ_00000448)
    title: food product origin geographic location
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0001207
    multivalued: false
    alias: food_origin
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
    pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
    structured_pattern:
      syntax: '^{text}: {text}, {text}$'
      interpolated: true
      partial_match: true
  food_prod:
    name: food_prod
    description: Descriptors of the food production system or of the agricultural
      environment and growing conditions related to the farm production system, such
      as wild caught, organic, free-range, industrial, dairy, beef,  domestic or cultivated
      food production. This field accepts terms listed under food production (http://purl.obolibrary.org/obo/FOODON_03530206).
      Multiple terms may apply and can be separated by pipes
    title: food production system characteristics
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0001211
    multivalued: true
    alias: food_prod
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - 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_product_type:
    name: food_product_type
    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-6-2-rc
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001184
    multivalued: false
    alias: food_product_type
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
  food_source:
    name: food_source
    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-6-2-rc
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0001139
    multivalued: false
    alias: food_source
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - food
    string_serialization: '{text}'
    slot_uri: MIXS:0001179
    multivalued: true
    alias: IFSAC_category
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
  intended_consumer:
    name: intended_consumer
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{integer}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001144
    multivalued: true
    alias: intended_consumer
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
  samp_purpose:
    name: samp_purpose
    description: The reason that the sample was collected
    title: purpose of sampling
    from_schema: https://w3id.org/mixs-6-2-rc
    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
    multivalued: false
    alias: samp_purpose
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
  animal_am:
    name: animal_am
    description: The name(s) (generic or brand) of the antimicrobial(s) given to the
      food animal within the last 30 days
    title: food animal antimicrobial
    examples:
    - value: tetracycline
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - animal
    - antimicrobial
    - food
    slot_uri: MIXS:0001243
    multivalued: false
    alias: animal_am
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    range: string
    required: false
    recommended: false
  animal_am_dur:
    name: animal_am_dur
    annotations:
      Expected_value:
        tag: Expected_value
        value: value
    description: The duration of time (days) that the antimicrobial was administered
      to the food animal
    title: food animal antimicrobial duration
    examples:
    - value: 3 days
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - animal
    - antimicrobial
    - duration
    - food
    - period
    string_serialization: '{float} {day}'
    slot_uri: MIXS:0001244
    multivalued: false
    alias: animal_am_dur
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    range: string
    required: false
    recommended: false
  animal_am_freq:
    name: animal_am_freq
    description: The frequency per day that the antimicrobial was adminstered to the
      food animal
    title: food animal antimicrobial frequency
    examples:
    - value: '1.5'
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - animal
    - antimicrobial
    - food
    - frequency
    slot_uri: MIXS:0001245
    alias: animal_am_freq
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    range: float
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  animal_am_route:
    name: animal_am_route
    description: The route by which the antimicrobial is adminstered into the body
      of the food animal
    title: food animal antimicrobial route of administration
    examples:
    - value: oral-feed
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - administration
    - animal
    - antimicrobial
    - food
    - route
    slot_uri: MIXS:0001246
    multivalued: false
    alias: animal_am_route
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    range: string
    required: false
    recommended: false
  animal_am_use:
    name: animal_am_use
    description: The prescribed intended use of or the condition treated by the antimicrobial
      given to the food animal by any route of administration
    title: food animal antimicrobial intended use
    examples:
    - value: shipping fever
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - animal
    - antimicrobial
    - food
    - use
    slot_uri: MIXS:0001247
    multivalued: false
    alias: animal_am_use
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    range: string
    required: false
    recommended: false
  animal_body_cond:
    name: animal_body_cond
    description: Body condition scoring is a production management tool used to evaluate
      overall health and nutritional needs of a food animal. Because there are different
      scoring systems, this field is restricted to three categories
    title: food animal body condition
    examples:
    - value: under conditioned
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - animal
    - body
    - condition
    - food
    slot_uri: MIXS:0001248
    multivalued: false
    alias: animal_body_cond
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    range: ANIMAL_BODY_COND_ENUM
    required: false
    recommended: false
  animal_diet:
    name: animal_diet
    annotations:
      Expected_value:
        tag: Expected_value
        value: text or FOODON_03309997
    description: If the isolate is from a food animal, the type of diet eaten by the
      food animal.  Please list the main food staple and the setting, if appropriate.  For
      a list of acceptable animal feed terms or categories, please see http://www.feedipedia.org.  Multiple
      terms may apply and can be separated by pipes |Food product for animal covers
      foods intended for consumption by domesticated animals. Consult http://purl.obolibrary.org/obo/FOODON_03309997.
      If the proper descriptor is not listed please use text to describe the food
      type. Multiple terms can be separated by one or more pipes. If the proper descriptor
      is not listed please use text to describe the food product type
    title: food animal source diet
    examples:
    - value: Hay [FOODON:03301763]
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - animal
    - diet
    - food
    - source
    string_serialization: '{text}'
    slot_uri: MIXS:0001130
    multivalued: true
    alias: animal_diet
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    range: string
    required: false
    recommended: false
  animal_feed_equip:
    name: animal_feed_equip
    annotations:
      Expected_value:
        tag: Expected_value
        value: EOL:0001757
    description: Description of the feeding equipment used for livestock. This field
      accepts terms listed under feed delivery (http://opendata.inra.fr/EOL/EOL_0001757).
      Multiple terms can be separated by pipes
    title: animal feeding equipment
    examples:
    - value: self feeding [EOL:0001645]| straight feed trough [EOL:0001661]
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - animal
    - equipment
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0001113
    multivalued: true
    alias: animal_feed_equip
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    range: string
    required: false
    recommended: false
  animal_group_size:
    name: animal_group_size
    description: The number of food animals of the same species that are maintained
      together as a unit, i.e. a herd or flock
    title: food animal group size
    examples:
    - value: '80'
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - animal
    - food
    - size
    slot_uri: MIXS:0001129
    multivalued: false
    alias: animal_group_size
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    range: integer
    required: false
    recommended: false
  animal_housing:
    name: animal_housing
    description: Description of the housing system of the livestock. This field accepts
      terms listed under terrestrial management housing system (http://opendata.inra.fr/EOL/EOL_0001605)
    title: animal housing system
    examples:
    - value: pen rearing system [EOL:0001636]
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - animal
    slot_uri: MIXS:0001180
    multivalued: true
    alias: animal_housing
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    range: string
    required: false
    recommended: false
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  animal_sex:
    name: animal_sex
    description: The sex and reproductive status of the food animal
    title: food animal source sex category
    examples:
    - value: castrated male
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - animal
    - food
    - source
    slot_uri: MIXS:0001249
    multivalued: false
    alias: animal_sex
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    range: ANIMAL_SEX_ENUM
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - density
    slot_uri: MIXS:0001194
    multivalued: false
    alias: bacterial_density
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  cons_food_stor_dur:
    name: cons_food_stor_dur
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: hours or days
    description: The storage duration of the food commodity by the consumer, prior
      to onset of illness or sample collection.  Indicate the timepoint written in
      ISO 8601 format
    title: food stored by consumer (storage duration)
    examples:
    - value: P5D
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - consumer
    - duration)
    - food
    - storage
    slot_uri: MIXS:0001195
    multivalued: false
    alias: cons_food_stor_dur
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
    structured_pattern:
      syntax: ^{duration}$
      interpolated: true
      partial_match: true
  cons_food_stor_temp:
    name: cons_food_stor_temp
    annotations:
      Expected_value:
        tag: Expected_value
        value: text or measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature at which food commodity was stored by the consumer, prior
      to onset of illness or sample collection
    title: food stored by consumer (storage temperature)
    examples:
    - value: 4 degree Celsius
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - consumer
    - food
    - storage
    - temperature
    string_serialization: '{float} {unit}|{text}'
    slot_uri: MIXS:0001196
    multivalued: false
    alias: cons_food_stor_temp
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  cons_purch_date:
    name: cons_purch_date
    description: The date a food product was purchased by consumer
    title: purchase date
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - date
    slot_uri: MIXS:0001197
    multivalued: false
    alias: cons_purch_date
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodHumanFoods
    range: datetime
    required: false
    recommended: false
  cons_qty_purchased:
    name: cons_qty_purchased
    description: The quantity of food purchased by consumer
    title: quantity purchased
    examples:
    - value: 5 cans
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - quantity
    slot_uri: MIXS:0001198
    multivalued: false
    alias: cons_qty_purchased
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{integer} {text}$
      interpolated: true
      partial_match: true
  cult_isol_date:
    name: cult_isol_date
    description: The datetime marking the end of a process in which a sample yields
      a positive result for the target microbial analyte(s) in the form of an isolated
      colony or colonies
    title: culture isolation date
    examples:
    - value: '2018-05-11T10:00:00+01:00'
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - culture
    - date
    - isolation
    slot_uri: MIXS:0001181
    multivalued: false
    alias: cult_isol_date
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: datetime
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - culture
    slot_uri: MIXS:0001117
    multivalued: false
    alias: cult_result
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: CULT_RESULT_ENUM
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - culture
    - organism
    slot_uri: MIXS:0001118
    multivalued: true
    alias: cult_result_org
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$
    structured_pattern:
      syntax: ^({termLabel} \[{termID}\])|{integer}$
      interpolated: true
      partial_match: true
  cult_target:
    name: cult_target
    annotations:
      Expected_value:
        tag: Expected_value
        value: NCIT:C14250 or NCBI taxid or culture independent
    description: The target microbial analyte in terms of investigation scope. This
      field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250).
      This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy
    title: culture target microbial analyte
    examples:
    - value: Listeria monocytogenes [NCIT:C86502]
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - culture
    - microbial
    - target
    string_serialization: '{termLabel} [{termID}]|{integer}'
    slot_uri: MIXS:0001119
    multivalued: true
    alias: cult_target
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0001177
    multivalued: false
    alias: enrichment_protocol
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: true
  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-6-2-rc
    keywords:
    - food
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001200
    multivalued: true
    alias: food_additive
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  food_contact_surf:
    name: food_contact_surf
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001131
    multivalued: true
    alias: food_contact_surf
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - food
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001132
    multivalued: false
    alias: food_contain_wrap
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - food
    - process
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001202
    multivalued: true
    alias: food_cooking_proc
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - food
    - geographic
    - location
    slot_uri: MIXS:0001203
    multivalued: true
    alias: food_dis_point
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    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-6-2-rc
    keywords:
    - food
    - geographic
    - location
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001204
    multivalued: true
    alias: food_dis_point_city
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - food
    - ingredient
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001205
    multivalued: true
    alias: food_ingredient
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - food
    - package
    slot_uri: MIXS:0001208
    multivalued: false
    alias: food_pack_capacity
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  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-6-2-rc
    keywords:
    - food
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001209
    multivalued: true
    alias: food_pack_integrity
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  food_pack_medium:
    name: food_pack_medium
    description: The medium in which the food is packed for preservation and handling
      or the medium surrounding homemade foods, e.g., peaches cooked in sugar syrup.
      The packing medium may provide a controlled environment for the food. It may
      also serve to improve palatability and consumer appeal.  This includes edible
      packing media (e.g. fruit juice), gas other than air (e.g. carbon dioxide),
      vacuum packed, or packed with aerosol propellant. This field accepts terms under
      food packing medium (http://purl.obolibrary.org/obo/FOODON_03480020). Multiple
      terms may apply and can be separated by pipes
    title: food packing medium
    examples:
    - value: packed in fruit juice [FOODON:03480039]
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001134
    multivalued: true
    alias: food_pack_medium
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - food
    - process
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001135
    multivalued: true
    alias: food_preserv_proc
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - food
    - material
    - prior
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001210
    multivalued: true
    alias: food_prior_contact
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - food
    - product
    slot_uri: MIXS:0001212
    multivalued: true
    alias: food_prod_synonym
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0001213
    multivalued: false
    alias: food_product_qual
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  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-6-2-rc
    keywords:
    - date
    - food
    - quality
    string_serialization: '[best by|best if used by|freeze by|use by]; date'
    slot_uri: MIXS:0001178
    multivalued: false
    alias: food_quality_date
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  food_source_age:
    name: food_source_age
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: days
    description: The age of the food source host organim. Depending on the type of
      host organism, age may be more appropriate to report in days, weeks, or years
    title: food source age
    comments:
    - ISO 8601 period or measurement value?
    examples:
    - value: 6 months
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - age
    - food
    - source
    slot_uri: MIXS:0001251
    alias: food_source_age
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  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-6-2-rc
    keywords:
    - food
    slot_uri: MIXS:0001214
    multivalued: false
    alias: food_trace_list
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: FOOD_TRACE_LIST_ENUM
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - food
    - method
    - transport
    slot_uri: MIXS:0001137
    multivalued: true
    alias: food_trav_mode
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  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-6-2-rc
    keywords:
    - food
    - transport
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001138
    multivalued: true
    alias: food_trav_vehic
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - food
    - process
    - treatment
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001140
    multivalued: true
    alias: food_treat_proc
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - food
    - term
    slot_uri: MIXS:0001215
    multivalued: true
    alias: HACCP_term
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  library_prep_kit:
    name: library_prep_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-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0001145
    multivalued: false
    alias: library_prep_kit
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - number
    string_serialization: '{integer}, {text}'
    slot_uri: MIXS:0001147
    multivalued: true
    alias: lot_number
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - culture
    - microbiological
    slot_uri: MIXS:0001216
    multivalued: false
    alias: microb_cult_med
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
    structured_pattern:
      syntax: ^{text}|({termLabel} \[{termID}\])$
      interpolated: true
      partial_match: true
  part_plant_animal:
    name: part_plant_animal
    annotations:
      Expected_value:
        tag: Expected_value
        value: FOODON:03420116
    description: The anatomical part of the organism being involved in food production
      or consumption; e.g., a carrot is the root of the plant (root vegetable). This
      field accepts terms listed under part of plant or animal (http://purl.obolibrary.org/obo/FOODON_03420116)
    title: part of plant or animal
    examples:
    - value: chuck [FOODON:03530021]
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - animal
    - plant
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001149
    multivalued: true
    alias: part_plant_animal
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0001152
    multivalued: true
    alias: repository_name
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0001153
    multivalued: true
    alias: samp_pooling
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - sample
    slot_uri: MIXS:0001226
    multivalued: false
    alias: samp_rep_biol
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_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-6-2-rc
    keywords:
    - sample
    slot_uri: MIXS:0001227
    multivalued: false
    alias: samp_rep_tech
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_source_mat_cat:
    name: samp_source_mat_cat
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0001154
    multivalued: false
    alias: samp_source_mat_cat
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  samp_stor_device:
    name: samp_stor_device
    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
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001228
    multivalued: false
    alias: samp_stor_device
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0001229
    multivalued: false
    alias: samp_stor_media
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
    structured_pattern:
      syntax: ^{text}|({termLabel} \[{termID}\])$
      interpolated: true
      partial_match: true
  samp_transport_dur:
    name: samp_transport_dur
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: days
    description: The duration of time from when the sample was collected until processed.
      Indicate the duration for which the sample was stored written in ISO 8601 format
    title: sample transport duration
    examples:
    - value: P10D
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - duration
    - period
    - sample
    - transport
    slot_uri: MIXS:0001231
    multivalued: false
    alias: samp_transport_dur
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
    structured_pattern:
      syntax: ^{duration}$
      interpolated: true
      partial_match: true
  samp_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-6-2-rc
    keywords:
    - sample
    - temperature
    - transport
    string_serialization: '{float} {unit} {text}'
    slot_uri: MIXS:0001232
    multivalued: false
    alias: samp_transport_temp
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - kit
    string_serialization: '{text}'
    slot_uri: MIXS:0001155
    multivalued: false
    alias: sequencing_kit
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - location
    slot_uri: MIXS:0001156
    multivalued: false
    alias: sequencing_location
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  serovar_or_serotype:
    name: serovar_or_serotype
    description: A characterization of a cell or microorganism based on the antigenic
      properties of the molecules on its surface. Indicate the name of a serovar or
      serotype of interest. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250).
      This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy
    title: serovar or serotype
    examples:
    - value: Escherichia coli strain O157:H7 [NCIT:C86883]
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0001157
    multivalued: true
    alias: serovar_or_serotype
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$
    structured_pattern:
      syntax: ^({termLabel} \[{termID}\])|{integer}$
      interpolated: true
      partial_match: true
  spikein_AMR:
    name: spikein_AMR
    annotations:
      Expected_value:
        tag: Expected_value
        value: measurement value ARO:3004299
    description: Qualitative description of a microbial response to antimicrobial
      agents. Bacteria may be susceptible or resistant to a broad range of antibiotic
      drugs or drug classes, with several intermediate states or phases. This field
      accepts terms under antimicrobial phenotype (http://purl.obolibrary.org/obo/ARO_3004299)
    title: antimicrobial phenotype of spike-in bacteria
    examples:
    - value: wild type [ARO:3004432]
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - antimicrobial
    - spike
    string_serialization: '{float} {unit};{termLabel} [{termID}]'
    slot_uri: MIXS:0001235
    multivalued: true
    alias: spikein_AMR
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  spikein_antibiotic:
    name: spikein_antibiotic
    annotations:
      Expected_value:
        tag: Expected_value
        value: drug name; concentration
    description: Antimicrobials used in research study to assess effects of exposure
      on microbiome of a specific site.  Please list antimicrobial, common name and/or
      class and concentration used for spike-in
    title: spike-in with antibiotics
    examples:
    - value: Tetracycline at 5 mg/ml
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - spike
    string_serialization: '{text} {integer}'
    slot_uri: MIXS:0001171
    multivalued: true
    alias: spikein_antibiotic
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  spikein_growth_med:
    name: spikein_growth_med
    description: A liquid or gel containing nutrients, salts, and other factors formulated
      to support the growth of microorganisms, cells, or plants (National Cancer Institute
      Thesaurus).  A growth medium is a culture medium which has the disposition to
      encourage growth of particular bacteria to the exclusion of others in the same
      growth environment.  In this case, list the culture medium used to propagate
      the spike-in bacteria during preparation of spike-in inoculum. This field accepts
      terms listed under microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067).
      If the proper descriptor is not listed please use text to describe the spike
      in growth media
    title: spike-in growth medium
    examples:
    - value: LB broth [MCO:0000036]
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - growth
    - spike
    slot_uri: MIXS:0001169
    multivalued: true
    alias: spikein_growth_med
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
    structured_pattern:
      syntax: ^{text}|({termLabel} \[{termID}\])$
      interpolated: true
      partial_match: true
  spikein_metal:
    name: spikein_metal
    annotations:
      Expected_value:
        tag: Expected_value
        value: heavy metal name or chemical symbol; concentration
    description: Heavy metals used in research study to assess effects of exposure
      on microbiome of a specific site.  Please list heavy metals and concentration
      used for spike-in
    title: spike-in with heavy metals
    examples:
    - value: Cd at 20 ppm
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - heavy
    - spike
    string_serialization: '{text} {integer}'
    slot_uri: MIXS:0001172
    multivalued: true
    alias: spikein_metal
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  spikein_org:
    name: spikein_org
    description: Taxonomic information about the spike-in organism(s). This field
      accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This
      field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy.
      Multiple terms can be separated by pipes
    title: spike in organism
    examples:
    - value: Listeria monocytogenes [NCIT:C86502]|28901
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - organism
    - spike
    slot_uri: MIXS:0001167
    multivalued: true
    alias: spikein_org
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$
    structured_pattern:
      syntax: ^({termLabel} \[{termID}\])|{integer}$
      interpolated: true
      partial_match: true
  spikein_serovar:
    name: spikein_serovar
    annotations:
      Expected_value:
        tag: Expected_value
        value: NCIT:C14250 or antigenic formula or serovar name
    description: Taxonomic information about the spike-in organism(s) at the serovar
      or serotype level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250).
      This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy.
      Multiple terms can be separated by pipes
    title: spike-in bacterial serovar or serotype
    examples:
    - value: Escherichia coli strain O157:H7 [NCIT:C86883]|83334
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - spike
    string_serialization: '{termLabel} [{termID}]|{integer}'
    slot_uri: MIXS:0001168
    multivalued: true
    alias: spikein_serovar
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  spikein_strain:
    name: spikein_strain
    annotations:
      Expected_value:
        tag: Expected_value
        value: NCIT:C14250 or NCBI taxid or text
    description: Taxonomic information about the spike-in organism(s) at the strain
      level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250).
      This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy.
      Multiple terms can be separated by pipes
    title: spike-in microbial strain
    examples:
    - value: '169963'
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - microbial
    - spike
    string_serialization: '{termLabel} [{termID}]|{integer}'
    slot_uri: MIXS:0001170
    multivalued: true
    alias: spikein_strain
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001236
    multivalued: true
    alias: study_design
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - duration
    - incubation
    - period
    slot_uri: MIXS:0001237
    multivalued: false
    alias: study_inc_dur
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
    structured_pattern:
      syntax: ^{duration}$
      interpolated: true
      partial_match: true
  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-6-2-rc
    keywords:
    - incubation
    - temperature
    slot_uri: MIXS:0001238
    multivalued: false
    alias: study_inc_temp
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  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-6-2-rc
    keywords:
    - duration
    - period
    - time
    slot_uri: MIXS:0001239
    multivalued: false
    alias: study_timecourse
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  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-6-2-rc
    keywords:
    - treatment
    string_serialization: '{text}|{termLabel} [{termID}]'
    slot_uri: MIXS:0001240
    multivalued: true
    alias: study_tmnt
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  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-6-2-rc
    keywords:
    - time
    slot_uri: MIXS:0001173
    multivalued: false
    alias: timepoint
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
    structured_pattern:
      syntax: ^{duration}$
      interpolated: true
      partial_match: true
  misc_param:
    name: misc_param
    annotations:
      Expected_value:
        tag: Expected_value
        value: parameter name;measurement value
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    examples:
    - value: Bicarbonate ion concentration;2075 micromole per kilogram
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - parameter
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    multivalued: true
    alias: misc_param
    owner: MimagFoodAnimalAndAnimalFeed
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
class_uri: MIXS:0010011_0016019