Class: Food-foodProductionFacilityMISAG

Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package food-food production facility

URI: MIXS:Food-foodProductionFacilityMISAG

Inheritance

• Food-foodProductionFacility
  • Food-foodProductionFacilityMISAG [ MISAG]

Slots

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...	MISAG
samp_taxon_id	1..1 String	NCBI taxon id of the sample	MISAG
project_name	1..1 String	Name of the project within which the sequencing was organized	MISAG
experimental_factor	0..1 recommended String	Experimental factors are essentially the variable aspects of an experiment de...	MISAG
lat_lon	1..1 String	The geographical origin of the sample as defined by latitude and longitude	Food-foodProductionFacility, MISAG
geo_loc_name	1..1 String	The geographical origin of the sample as defined by the country or sea name f...	Food-foodProductionFacility, MISAG
collection_date	1..1 Date	The time of sampling, either as an instance (single point in time) or interva...	Food-foodProductionFacility, MISAG
neg_cont_type	0..1 recommended NegContTypeEnum	The substance or equipment used as a negative control in an investigation	MISAG
pos_cont_type	0..1 recommended String	The substance, mixture, product, or apparatus used to verify that a process w...	MISAG
env_broad_scale	1..1 String	Report the major environmental system the sample or specimen came from	Food-foodProductionFacility, MISAG
env_local_scale	1..1 String	Report the entity or entities which are in the sample or specimen’s local vic...	Food-foodProductionFacility, MISAG
env_medium	1..1 String	Report the environmental material(s) immediately surrounding the sample or sp...	Food-foodProductionFacility, MISAG
ref_biomaterial	0..1 String	Primary publication if isolated before genome publication; otherwise, primary...	MISAG
source_mat_id	0..1 recommended String	A unique identifier assigned to a material sample (as defined by http://rs	MISAG
rel_to_oxygen	0..1 RelToOxygenEnum	Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ...	MISAG
samp_collec_device	0..1 recommended String	The device used to collect an environmental sample	MISAG
samp_collec_method	0..1 recommended String	The method employed for collecting the sample	MISAG
samp_mat_process	0..1 recommended String	A brief description of any processing applied to the sample during or after r...	MISAG
size_frac	0..1 String	Filtering pore size used in sample preparation	MISAG
samp_size	0..1 recommended QuantityValue	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...	MISAG
samp_vol_we_dna_ext	0..1 QuantityValue	Volume (ml) or mass (g) of total collected sample processed for DNA extractio...	MISAG
nucl_acid_ext	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...	MISAG
nucl_acid_amp	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...	MISAG
lib_size	0..1 recommended Integer	Total number of clones in the library prepared for the project	MISAG
lib_reads_seqd	0..1 recommended Integer	Total number of clones sequenced from the library	MISAG
lib_layout	0..1 recommended LibLayoutEnum	Specify whether to expect single, paired, or other configuration of reads	MISAG
lib_vector	0..1 recommended String	Cloning vector type(s) used in construction of libraries	MISAG
lib_screen	0..1 recommended String	Specific enrichment or screening methods applied before and/or after creating...	MISAG
mid	0..1 recommended String	Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe...	MISAG
adapters	0..1 recommended String	Adapters provide priming sequences for both amplification and sequencing of t...	MISAG
seq_meth	1..1 String	Sequencing machine used	MISAG
tax_ident	1..1 TaxIdentEnum	The phylogenetic marker(s) used to assign an organism name to the SAG or MAG	MISAG
assembly_qual	1..1 AssemblyQualEnum	The assembly quality category is based on sets of criteria outlined for each ...	MISAG
assembly_name	0..1 recommended String	Name/version of the assembly provided by the submitter that is used in the ge...	MISAG
assembly_software	1..1 String	Tool(s) used for assembly, including version number and parameters	MISAG
annot	0..1 String	Tool used for annotation, or for cases where annotation was provided by a com...	MISAG
number_contig	0..1 Integer	Total number of contigs in the cleaned/submitted assembly that makes up a giv...	MISAG
feat_pred	0..1 String	Method used to predict UViGs features such as ORFs, integration site, etc	MISAG
ref_db	0..1 String	List of database(s) used for ORF annotation, along with version number and re...	MISAG
sim_search_meth	0..1 String	Tool used to compare ORFs with database, along with version and cutoffs used	MISAG
tax_class	0..1 String	Method used for taxonomic classification, along with reference database used,...	MISAG
x_16s_recover	0..1 String	Can a 16S gene be recovered from the submitted SAG or MAG?	MISAG
x_16s_recover_software	0..1 String	Tools used for 16S rRNA gene extraction	MISAG
trnas	0..1 Integer	The total number of tRNAs identified from the SAG or MAG	MISAG
trna_ext_software	0..1 String	Tools used for tRNA identification	MISAG
compl_score	1..1 String	Completeness score is typically based on either the fraction of markers found...	MISAG
compl_software	1..1 String	Tools used for completion estimate, i	MISAG
compl_appr	0..1 ComplApprEnum	The approach used to determine the completeness of a given genomic assembly, ...	MISAG
contam_score	1..1 String	The contamination score is based on the fraction of single-copy genes that ar...	MISAG
contam_screen_input	0..1 String	The type of sequence data used as input	MISAG
contam_screen_param	0..1 String	Specific parameters used in the decontamination sofware, such as reference da...	MISAG
decontam_software	0..1 DecontamSoftwareEnum	Tool(s) used in contamination screening	MISAG
sort_tech	1..1 SortTechEnum	Method used to sort/isolate cells or particles of interest	MISAG
single_cell_lysis_appr	1..1 SingleCellLysisApprEnum	Method used to free DNA from interior of the cell(s) or particle(s)	MISAG
single_cell_lysis_prot	0..1 String	Name of the kit or standard protocol used for cell(s) or particle(s) lysis	MISAG
wga_amp_appr	1..1 String	Method used to amplify genomic DNA in preparation for sequencing	MISAG
wga_amp_kit	0..1 String	Kit used to amplify genomic DNA in preparation for sequencing	MISAG
associated_resource	0..1 recommended String	A related resource that is referenced, cited, or otherwise associated to the ...	MISAG
sop	0..1 recommended String	Standard operating procedures used in assembly and/or annotation of genomes, ...	MISAG
depth	0..1 QuantityValue	The vertical distance below local surface, e	Food-foodProductionFacility
alt	0..1 QuantityValue	Altitude is a term used to identify heights of objects such as airplanes, spa...	Food-foodProductionFacility
elev	0..1 QuantityValue	Elevation of the sampling site is its height above a fixed reference point, m...	Food-foodProductionFacility
temp	0..1 QuantityValue	Temperature of the sample at the time of sampling	Food-foodProductionFacility
samp_collect_device	0..1 String	The device used to collect an environmental sample	Food-foodProductionFacility
organism_count	0..* OrganismCountEnum	Total cell count of any organism (or group of organisms) per gram, volume or ...	Food-foodProductionFacility
samp_stor_temp	0..1 QuantityValue	Temperature at which sample was stored, e	Food-foodProductionFacility
samp_stor_dur	0..1 String	Duration for which the sample was stored	Food-foodProductionFacility
air_temp	0..1 QuantityValue	Temperature of the air at the time of sampling	Food-foodProductionFacility
room_dim	0..1 String	The length, width and height of sampling room	Food-foodProductionFacility
freq_clean	0..1 FreqCleanEnum	The number of times the sample location is cleaned	Food-foodProductionFacility
samp_room_id	0..1 Integer	Sampling room number	Food-foodProductionFacility
pool_dna_extracts	0..1 String	Indicate whether multiple DNA extractions were mixed	Food-foodProductionFacility
samp_stor_loc	0..1 String	Location at which sample was stored, usually name of a specific freezer/room	Food-foodProductionFacility
surf_material	0..1 SurfMaterialEnum	Surface materials at the point of sampling	Food-foodProductionFacility
indoor_surf	0..1 IndoorSurfEnum	Type of indoor surface	Food-foodProductionFacility
avg_occup	0..1 Double	Daily average occupancy of room	Food-foodProductionFacility
samp_floor	0..1 SampFloorEnum	The floor of the building, where the sampling room is located	Food-foodProductionFacility
genetic_mod	0..1 String	Genetic modifications of the genome of an organism, which may occur naturally...	Food-foodProductionFacility
coll_site_geo_feat	1..1 String	Text or terms that describe the geographic feature where the food sample was ...	Food-foodProductionFacility
samp_source_mat_cat	1..1 String	This is the scientific role or category that the subject organism or material...	Food-foodProductionFacility
samp_type	1..1 String	The type of material from which the sample was obtained	Food-foodProductionFacility
samp_stor_media	1..1 String	The liquid that is added to the sample collection device prior to sampling	Food-foodProductionFacility
samp_stor_device	1..1 String	The container used to store the sample	Food-foodProductionFacility
food_product_type	1..* String	A food product type is a class of food products that is differentiated by its...	Food-foodProductionFacility
IFSAC_category	1..* String	The IFSAC food categorization scheme has five distinct levels to which foods ...	Food-foodProductionFacility
food_product_qual	1..1 String	Descriptors for describing food visually or via other senses, which is useful...	Food-foodProductionFacility
food_contact_surf	1..* String	The specific container or coating materials in direct contact with the food	Food-foodProductionFacility
facility_type	0..* FacilityTypeEnum	Establishment details about the type of facility where the sample was taken	Food-foodProductionFacility
food_trav_mode	0..* String	A descriptor for the method of movement of food commodity along the food dist...	Food-foodProductionFacility
food_trav_vehic	0..* String	A descriptor for the mobile machine which is used to transport food commoditi...	Food-foodProductionFacility
samp_transport_dur	0..1 QuantityValue	The duration of time from when the sample was collected until processed	Food-foodProductionFacility
samp_transport_temp	0..1 String	Temperature at which sample was transported, e	Food-foodProductionFacility
samp_collect_method	0..1 String	The method employed for collecting the sample	Food-foodProductionFacility
num_samp_collect	0..1 QuantityValue	The number of samples collected during the current sampling event	Food-foodProductionFacility
lot_number	0..* String	A distinctive alpha-numeric identification code assigned by the manufacturer ...	Food-foodProductionFacility
hygienic_area	0..1 String	The subdivision of areas within a food production facility according to hygie...	Food-foodProductionFacility
env_monitoring_zone	0..1 String	An environmental monitoring zone is a formal designation as part of an enviro...	Food-foodProductionFacility
area_samp_size	0..1 String	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...	Food-foodProductionFacility
samp_surf_moisture	0..* SampSurfMoistureEnum	Degree of water held on a sampled surface	Food-foodProductionFacility
samp_loc_condition	0..1 SampLocConditionEnum	The condition of the sample location at the time of sampling	Food-foodProductionFacility
biocide_used	0..* String	Substance intended for preventing, neutralizing, destroying, repelling, or mi...	Food-foodProductionFacility
ster_meth_samp_room	0..* String	The method used to sterilize the sampling room	Food-foodProductionFacility
enrichment_protocol	0..1 String	The microbiological workflow or protocol followed to test for the presence or...	Food-foodProductionFacility
cult_target	0..* String	The target microbial analyte in terms of investigation scope	Food-foodProductionFacility
microb_cult_med	0..1 String	A culture medium used to select for, grow, and maintain prokaryotic microorga...	Food-foodProductionFacility
timepoint	0..1 Double	Time point at which a sample or observation is made or taken from a biomateri...	Food-foodProductionFacility
bacterial_density	0..1 QuantityValue	Number of bacteria in sample, as defined by bacteria density (http://purl	Food-foodProductionFacility
cult_isol_date	0..1 Date	A culture isolation date is a date-time entity marking the end of a process i...	Food-foodProductionFacility
cult_result	0..1 CultResultEnum	Any result of a bacterial culture experiment reported as a binary assessment ...	Food-foodProductionFacility
cult_result_org	0..* String	Taxonomic information about the cultured organism(s)	Food-foodProductionFacility
samp_pooling	0..* String	Physical combination of several instances of like material, e	Food-foodProductionFacility
samp_purpose	0..1 String	The reason that the sample was collected	Food-foodProductionFacility
samp_rep_tech	0..1 QuantityValue	Repeated measurements of the same sample that show independent measures of th...	Food-foodProductionFacility
samp_rep_biol	0..1 QuantityValue	Measurements of biologically distinct samples that show biological variation	Food-foodProductionFacility
samp_transport_cont	0..1 SampTransportContEnum	Conatiner in which the sample was stored during transport	Food-foodProductionFacility
study_design	0..* String	A plan specification comprised of protocols (which may specify how and what k...	Food-foodProductionFacility
nucl_acid_ext_kit	0..* String	The name of the extraction kit used to recover the nucleic acid fraction of a...	Food-foodProductionFacility
library_prep_kit	0..1 String	Packaged kits (containing adapters, indexes, enzymes, buffers etc	Food-foodProductionFacility
sequencing_kit	0..1 String	Pre-filled, ready-to-use reagent cartridges	Food-foodProductionFacility
sequencing_location	0..1 String	The location the sequencing run was performed	Food-foodProductionFacility
study_inc_temp	0..1 QuantityValue	Sample incubation temperature if unpublished or unvalidated method is used	Food-foodProductionFacility
study_inc_dur	0..1 QuantityValue	Sample incubation duration if unpublished or unvalidated method is used	Food-foodProductionFacility
study_timecourse	0..1 QuantityValue	For time-course research studies involving samples of the food commodity, ind...	Food-foodProductionFacility
study_tmnt	0..* String	A process in which the act is intended to modify or alter some other material...	Food-foodProductionFacility
food_source	0..1 String	Type of plant or animal from which the food product or its major ingredient i...	Food-foodProductionFacility
food_dis_point	0..* String	A reference to a place on the Earth, by its name or by its geographical locat...	Food-foodProductionFacility
food_dis_point_city	0..1 String	A reference to a place on the Earth, by its name or by its geographical locat...	Food-foodProductionFacility
food_origin	0..1 String	A reference to a place on the Earth, by its name or by its geographical locat...	Food-foodProductionFacility
food_prod_synonym	0..* String	Other names by which the food product is known by (e	Food-foodProductionFacility
food_additive	0..* String	A substance or substances added to food to maintain or improve safety and fre...	Food-foodProductionFacility
food_trace_list	0..1 FoodTraceListEnum	The FDA is proposing to establish additional traceability recordkeeping requi...	Food-foodProductionFacility
part_plant_animal	0..* String	The anatomical part of the organism being involved in food production or cons...	Food-foodProductionFacility
food_ingredient	0..* String	In this field, please list individual ingredients for multi-component food [F...	Food-foodProductionFacility
spec_intended_cons	0..* String	Food consumer type, human or animal, for which the food product is produced a...	Food-foodProductionFacility
HACCP_term	0..* String	Hazard Analysis Critical Control Points (HACCP) food safety terms; This field...	Food-foodProductionFacility
dietary_claim_use	0..* String	These descriptors are used either for foods intended for special dietary use ...	Food-foodProductionFacility
food_allergen_label	0..* String	A label indication that the product contains a recognized allergen	Food-foodProductionFacility
food_prod_char	0..* String	Descriptors of the food production system such as wild caught, free-range, or...	Food-foodProductionFacility
prod_label_claims	0..* String	Labeling claims containing descriptors such as wild caught, free-range, organ...	Food-foodProductionFacility
food_name_status	0..1 String	A datum indicating that use of a food product name is regulated in some legal...	Food-foodProductionFacility
food_preserv_proc	0..* String	The methods contributing to the prevention or retardation of microbial, enzym...	Food-foodProductionFacility
food_cooking_proc	0..* String	The transformation of raw food by the application of heat	Food-foodProductionFacility
food_treat_proc	0..* String	Used to specifically characterize a food product based on the treatment or pr...	Food-foodProductionFacility
food_contain_wrap	0..1 String	Type of container or wrapping defined by the main container material, the con...	Food-foodProductionFacility
food_pack_capacity	0..1 QuantityValue	The maximum number of product units within a package	Food-foodProductionFacility
food_pack_medium	0..* String	The medium in which the food is packed for preservation and handling or the m...	Food-foodProductionFacility
food_prior_contact	0..* String	The material the food contacted (e	Food-foodProductionFacility
food_prod	0..* String	Descriptors of the food production system or of the agricultural environment ...	Food-foodProductionFacility
food_quality_date	0..1 String	The date recommended for the use of the product while at peak quality, this d...	Food-foodProductionFacility
repository_name	0..* String	The name of the institution where the sample or DNA extract is held or "sampl...	Food-foodProductionFacility
intended_consumer	0..* String	Food consumer type, human or animal, for which the food product is produced a...	Food-foodProductionFacility
food_pack_integrity	0..* String	A term label and term id to describe the state of the packing material and te...	Food-foodProductionFacility
misc_param	0..* String	Any other measurement performed or parameter collected, that is not listed he...	Food-foodProductionFacility

Identifier and Mapping Information

Schema Source

• from schema: http://w3id.org/mixs

Mappings

Mapping Type	Mapped Value
self	MIXS:Food-foodProductionFacilityMISAG
native	MIXS:Food-foodProductionFacilityMISAG

LinkML Source

Direct

name: food-food production facility MISAG
description: Combinatorial checklist Minimum Information About a Single Amplified
  Genome with environmental package food-food production facility
from_schema: http://w3id.org/mixs
is_a: food-food production facility
mixins:
- MISAG

Induced

name: food-food production facility MISAG
description: Combinatorial checklist Minimum Information About a Single Amplified
  Genome with environmental package food-food production facility
from_schema: http://w3id.org/mixs
is_a: food-food production facility
mixins:
- MISAG
attributes:
  samp_name:
    name: samp_name
    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
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{text}'
    slot_uri: MIXS:0001107
    multivalued: false
    alias: samp_name
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: 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
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{text} [NCBI:txid]'
    slot_uri: MIXS:0001320
    multivalued: false
    alias: samp_taxon_id
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
  project_name:
    name: project_name
    description: Name of the project within which the sequencing was organized
    title: project name
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{text}'
    slot_uri: MIXS:0000092
    multivalued: false
    alias: project_name
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
  experimental_factor:
    name: experimental_factor
    description: Experimental factors are essentially the variable aspects of an experiment
      design which 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). For
      a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;
      for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
    title: experimental factor
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000008
    multivalued: false
    alias: experimental_factor
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
    recommended: true
  lat_lon:
    name: lat_lon
    description: The geographical origin of the sample as defined by latitude and
      longitude. The values should be reported in decimal degrees and in WGS84 system
    title: geographic location (latitude and longitude)
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{float} {float}'
    slot_uri: MIXS:0000009
    multivalued: false
    alias: lat_lon
    owner: food-food production facility MISAG
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: 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)
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{term}: {term}, {text}'
    slot_uri: MIXS:0000010
    multivalued: false
    alias: geo_loc_name
    owner: food-food production facility MISAG
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: 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
    from_schema: http://w3id.org/mixs
    is_a: environment field
    slot_uri: MIXS:0000011
    multivalued: false
    alias: collection_date
    owner: food-food production facility MISAG
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: date
    required: true
  neg_cont_type:
    name: neg_cont_type
    description: The substance or equipment used as a negative control in an investigation
    title: negative control type
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    slot_uri: MIXS:0001321
    multivalued: false
    alias: neg_cont_type
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: neg_cont_type_enum
    recommended: true
  pos_cont_type:
    name: pos_cont_type
    description: The substance, mixture, product, or apparatus used to verify that
      a process which is part of an investigation delivers a true positive.
    title: positive control type
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    multivalued: false
    alias: pos_cont_type
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  env_broad_scale:
    name: env_broad_scale
    description: 'Report the major environmental system the sample or specimen came
      from. The system(s) identified should have a coarse spatial grain, to provide
      the general environmental context of where the sampling was done (e.g. in the
      desert or a rainforest). We recommend using subclasses of EnvO’s biome class:  http://purl.obolibrary.org/obo/ENVO_00000428.
      EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: broad-scale environmental context
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    multivalued: false
    alias: env_broad_scale
    owner: food-food production facility MISAG
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  env_local_scale:
    name: env_local_scale
    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
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000013
    multivalued: false
    alias: env_local_scale
    owner: food-food production facility MISAG
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  env_medium:
    name: env_medium
    description: 'Report the environmental material(s) immediately surrounding the
      sample or specimen at the time of sampling. We recommend using subclasses of
      ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
      documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
      . Terms from other OBO ontologies are permissible as long as they reference
      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
      (e.g. a tree, a leaf, a table top).'
    title: environmental medium
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000014
    multivalued: false
    alias: env_medium
    owner: food-food production facility MISAG
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - 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: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000025
    multivalued: false
    alias: ref_biomaterial
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{text}'
    slot_uri: MIXS:0000026
    multivalued: false
    alias: source_mat_id
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  rel_to_oxygen:
    name: rel_to_oxygen
    description: Is this organism an aerobe, anaerobe? Please note that aerobic and
      anaerobic are valid descriptors for microbial environments
    title: relationship to oxygen
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000015
    multivalued: false
    alias: rel_to_oxygen
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS bacteria
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    range: rel_to_oxygen_enum
    required: false
  samp_collec_device:
    name: samp_collec_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
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000002
    multivalued: false
    alias: samp_collec_device
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  samp_collec_method:
    name: samp_collec_method
    description: The method employed for collecting the sample.
    title: sample collection method
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001225
    multivalued: false
    alias: samp_collec_method
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  samp_mat_process:
    name: samp_mat_process
    description: A brief description of any processing applied to the sample during
      or after retrieving the sample from environment, or a link to the relevant protocol(s)
      performed.
    title: sample material processing
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{text}'
    slot_uri: MIXS:0000016
    multivalued: false
    alias: samp_mat_process
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  size_frac:
    name: size_frac
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    multivalued: false
    alias: size_frac
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000001
    multivalued: false
    alias: samp_size
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: quantity value
    required: false
    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: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000111
    multivalued: false
    alias: samp_vol_we_dna_ext
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: quantity value
    required: 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: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000037
    multivalued: false
    alias: nucl_acid_ext
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
    recommended: true
  nucl_acid_amp:
    name: nucl_acid_amp
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the enzymatic amplification (PCR,
      TMA, NASBA) of specific nucleic acids
    title: nucleic acid amplification
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000038
    multivalued: false
    alias: nucl_acid_amp
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  lib_size:
    name: lib_size
    description: Total number of clones in the library prepared for the project
    title: library size
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000039
    multivalued: false
    alias: lib_size
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: integer
    recommended: true
  lib_reads_seqd:
    name: lib_reads_seqd
    description: Total number of clones sequenced from the library
    title: library reads sequenced
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000040
    multivalued: false
    alias: lib_reads_seqd
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: integer
    recommended: true
  lib_layout:
    name: lib_layout
    description: Specify whether to expect single, paired, or other configuration
      of reads
    title: library layout
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000041
    multivalued: false
    alias: lib_layout
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: lib_layout_enum
    recommended: true
  lib_vector:
    name: lib_vector
    description: Cloning vector type(s) used in construction of libraries
    title: library vector
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000042
    multivalued: false
    alias: lib_vector
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  lib_screen:
    name: lib_screen
    description: Specific enrichment or screening methods applied before and/or after
      creating libraries
    title: library screening strategy
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000043
    multivalued: false
    alias: lib_screen
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  mid:
    name: mid
    description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
      used to specifically tag unique samples in a sequencing run. Sequence should
      be reported in uppercase letters
    title: multiplex identifiers
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{dna}'
    slot_uri: MIXS:0000047
    multivalued: false
    alias: mid
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    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: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{dna};{dna}'
    slot_uri: MIXS:0000048
    multivalued: false
    alias: adapters
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  seq_meth:
    name: seq_meth
    description: Sequencing machine used. Where possible the term should be taken
      from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).
    title: sequencing method
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000050
    multivalued: false
    alias: seq_meth
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: 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: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000053
    multivalued: false
    alias: tax_ident
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MISAG
    - MIMAG
    - MIUVIG
    range: tax_ident_enum
    required: true
  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: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000056
    multivalued: false
    alias: assembly_qual
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MISAG
    - MIMAG
    - MIUVIG
    range: assembly_qual_enum
    required: 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: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text} {text}'
    slot_uri: MIXS:0000057
    multivalued: false
    alias: assembly_name
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  assembly_software:
    name: assembly_software
    description: Tool(s) used for assembly, including version number and parameters
    title: assembly software
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{software};{version};{parameters}'
    slot_uri: MIXS:0000058
    multivalued: false
    alias: assembly_software
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    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: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000059
    multivalued: false
    alias: annot
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000060
    multivalued: false
    alias: number_contig
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MISAG
    - MIMAG
    - MIUVIG
    range: integer
    required: false
  feat_pred:
    name: feat_pred
    description: Method used to predict UViGs features such as ORFs, integration site,
      etc.
    title: feature prediction
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{software};{version};{parameters}'
    slot_uri: MIXS:0000061
    multivalued: false
    alias: feat_pred
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{database};{version};{reference}'
    slot_uri: MIXS:0000062
    multivalued: false
    alias: ref_db
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{software};{version};{parameters}'
    slot_uri: MIXS:0000063
    multivalued: false
    alias: sim_search_meth
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000064
    multivalued: false
    alias: tax_class
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  x_16s_recover:
    name: x_16s_recover
    description: Can a 16S gene be recovered from the submitted SAG or MAG?
    title: 16S recovered
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{boolean}'
    slot_uri: MIXS:0000065
    multivalued: false
    alias: x_16s_recover
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MISAG
    - MIMAG
    range: string
    required: false
  x_16s_recover_software:
    name: x_16s_recover_software
    description: Tools used for 16S rRNA gene extraction
    title: 16S recovery software
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{software};{version};{parameters}'
    slot_uri: MIXS:0000066
    multivalued: false
    alias: x_16s_recover_software
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MISAG
    - MIMAG
    range: string
    required: false
  trnas:
    name: trnas
    description: The total number of tRNAs identified from the SAG or MAG
    title: number of standard tRNAs extracted
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000067
    multivalued: false
    alias: trnas
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MISAG
    - MIMAG
    - MIUVIG
    range: integer
    required: false
  trna_ext_software:
    name: trna_ext_software
    description: Tools used for tRNA identification
    title: tRNA extraction software
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{software};{version};{parameters}'
    slot_uri: MIXS:0000068
    multivalued: false
    alias: trna_ext_software
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000069
    multivalued: false
    alias: compl_score
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
    pattern: ^(high|med|low);(0|([0-9]{1,2})|100)%$
  compl_software:
    name: compl_software
    description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
    title: completeness software
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{software};{version}'
    slot_uri: MIXS:0000070
    multivalued: false
    alias: compl_software
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: 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: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000071
    multivalued: false
    alias: compl_appr
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MISAG
    - MIMAG
    - MIUVIG
    range: compl_appr_enum
    required: false
  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: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{float} percentage'
    slot_uri: MIXS:0000072
    multivalued: false
    alias: contam_score
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MISAG
    - MIMAG
    range: string
    required: true
  contam_screen_input:
    name: contam_screen_input
    description: The type of sequence data used as input
    title: contamination screening input
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '[reads| contigs]'
    slot_uri: MIXS:0000005
    multivalued: false
    alias: contam_screen_input
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MISAG
    - MIMAG
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000073
    multivalued: false
    alias: contam_screen_param
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MISAG
    - MIMAG
    range: string
    required: false
    pattern: ^(ref db|kmer|coverage|combination);.+
  decontam_software:
    name: decontam_software
    description: Tool(s) used in contamination screening
    title: decontamination software
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000074
    multivalued: false
    alias: decontam_software
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MISAG
    - MIMAG
    range: decontam_software_enum
    required: false
  sort_tech:
    name: sort_tech
    description: Method used to sort/isolate cells or particles of interest
    title: sorting technology
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000075
    multivalued: false
    alias: sort_tech
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MISAG
    - MIUVIG
    range: sort_tech_enum
    required: true
  single_cell_lysis_appr:
    name: single_cell_lysis_appr
    description: Method used to free DNA from interior of the cell(s) or particle(s)
    title: single cell or viral particle lysis approach
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000076
    multivalued: false
    alias: single_cell_lysis_appr
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MISAG
    - MIUVIG
    range: single_cell_lysis_appr_enum
    required: true
  single_cell_lysis_prot:
    name: single_cell_lysis_prot
    description: Name of the kit or standard protocol used for cell(s) or particle(s)
      lysis
    title: single cell or viral particle lysis kit protocol
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000054
    multivalued: false
    alias: single_cell_lysis_prot
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MISAG
    - MIUVIG
    range: string
    required: false
  wga_amp_appr:
    name: wga_amp_appr
    description: Method used to amplify genomic DNA in preparation for sequencing
    title: WGA amplification approach
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '[pcr based|mda based]'
    slot_uri: MIXS:0000055
    multivalued: false
    alias: wga_amp_appr
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MISAG
    - MIUVIG
    range: string
    required: true
  wga_amp_kit:
    name: wga_amp_kit
    description: Kit used to amplify genomic DNA in preparation for sequencing
    title: WGA amplification kit
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000006
    multivalued: false
    alias: wga_amp_kit
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MISAG
    - MIUVIG
    range: string
    required: false
  associated resource:
    name: associated resource
    description: A related resource that is referenced, cited, or otherwise associated
      to the sequence.
    title: relevant electronic resources
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID} | {DOI} | {URL}'
    slot_uri: MIXS:0000091
    multivalued: false
    alias: associated_resource
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    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: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000090
    multivalued: false
    alias: sop
    owner: food-food production facility MISAG
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  depth:
    name: depth
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: The vertical distance below local surface, e.g. 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: http://w3id.org/mixs
    aliases:
    - depth
    is_a: environment field
    slot_uri: MIXS:0000018
    multivalued: false
    alias: depth
    owner: food-food production facility MISAG
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
  alt:
    name: alt
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: Altitude is a term used to identify heights of objects such as airplanes,
      space shuttles, rockets, atmospheric balloons and heights of places such as
      atmospheric layers and clouds. It is used to measure the height of an object
      which is above the earth's surface. In this context, the altitude measurement
      is the vertical distance between the earth's surface above sea level and the
      sampled position in the air
    title: altitude
    examples:
    - value: 100 meter
    from_schema: http://w3id.org/mixs
    aliases:
    - altitude
    is_a: environment field
    slot_uri: MIXS:0000094
    multivalued: false
    alias: alt
    owner: food-food production facility MISAG
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
  elev:
    name: elev
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit.
    title: elevation
    examples:
    - value: 100 meter
    from_schema: http://w3id.org/mixs
    aliases:
    - elevation
    is_a: environment field
    slot_uri: MIXS:0000093
    multivalued: false
    alias: elev
    owner: food-food production facility MISAG
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
  temp:
    name: temp
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
      preferred_unit:
        tag: preferred_unit
        value: degree Celsius
    description: Temperature of the sample at the time of sampling.
    title: temperature
    examples:
    - value: 25 degree Celsius
    from_schema: http://w3id.org/mixs
    aliases:
    - temperature
    is_a: environment field
    slot_uri: MIXS:0000113
    multivalued: false
    alias: temp
    owner: food-food production facility MISAG
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
  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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000002
    multivalued: false
    alias: samp_collect_device
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  organism_count:
    name: organism_count
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000103
    multivalued: true
    alias: organism_count
    owner: food-food production facility MISAG
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - built environment
    - air
    - agriculture
    range: organism_count_enum
    required: false
  samp_stor_temp:
    name: samp_stor_temp
    description: Temperature at which sample was stored, e.g. -80 degree Celsius.
    title: sample storage temperature
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000110
    multivalued: false
    alias: samp_stor_temp
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: quantity value
    required: false
  samp_stor_dur:
    name: samp_stor_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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{duration}'
    slot_uri: MIXS:0000116
    multivalued: false
    alias: samp_stor_dur
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: false
  air_temp:
    name: air_temp
    description: Temperature of the air at the time of sampling
    title: air temperature
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000124
    multivalued: false
    alias: air_temp
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    - built environment
    range: quantity value
    required: false
  room_dim:
    name: room_dim
    description: The length, width and height of sampling room
    title: room dimensions
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'
    slot_uri: MIXS:0000192
    multivalued: false
    alias: room_dim
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    - built environment
    range: string
    required: false
  freq_clean:
    name: freq_clean
    description: The number of times the sample location is cleaned. Frequency of
      cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.
    title: frequency of cleaning
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000226
    multivalued: false
    alias: freq_clean
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    - built environment
    range: freq_clean_enum
    required: false
  samp_room_id:
    name: samp_room_id
    description: Sampling room number. This ID should be consistent with the designations
      on the building floor plans
    title: sampling room ID or name
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000244
    multivalued: false
    alias: samp_room_id
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    - built environment
    range: integer
    required: false
  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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{boolean};{integer}'
    slot_uri: MIXS:0000325
    multivalued: false
    alias: pool_dna_extracts
    owner: food-food production facility MISAG
    domain_of:
    - soil
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  samp_stor_loc:
    name: samp_stor_loc
    description: Location at which sample was stored, usually name of a specific freezer/room.
      Indicate the location name.
    title: sample storage location
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000755
    multivalued: false
    alias: samp_stor_loc
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: false
  surf_material:
    name: surf_material
    description: Surface materials at the point of sampling
    title: surface material
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000758
    multivalued: false
    alias: surf_material
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    - built environment
    range: surf_material_enum
    required: false
  indoor_surf:
    name: indoor_surf
    description: Type of indoor surface
    title: indoor surface
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000764
    multivalued: false
    alias: indoor_surf
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    - built environment
    range: indoor_surf_enum
    required: false
  avg_occup:
    name: avg_occup
    description: Daily average occupancy of room. Indicate the number of person(s)
      daily occupying the sampling room.
    title: average daily occupancy
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000775
    multivalued: false
    alias: avg_occup
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    - built environment
    range: double
    required: false
  samp_floor:
    name: samp_floor
    description: The floor of the building, where the sampling room is located
    title: sampling floor
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000828
    multivalued: false
    alias: samp_floor
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    - built environment
    range: samp_floor_enum
    required: false
  genetic_mod:
    name: genetic_mod
    description: Genetic modifications of the genome of an organism, which may occur
      naturally by spontaneous mutation, or be introduced by some experimental means,
      e.g. specification of a transgene or the gene knocked-out or details of transient
      transfection
    title: genetic modification
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0000859
    multivalued: false
    alias: genetic_mod
    owner: food-food production facility MISAG
    domain_of:
    - plant-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - agriculture
    range: string
    required: false
  coll_site_geo_feat:
    name: coll_site_geo_feat
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001183
    multivalued: false
    alias: coll_site_geo_feat
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: 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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001154
    multivalued: false
    alias: samp_source_mat_cat
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: true
  samp_type:
    name: samp_type
    description: The type of material from which the sample was obtained. For the
      Hydrocarbon package, samples include types like core, rock trimmings, drill
      cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid,
      produced water, injected water, swabs, etc. For the Food Package, samples are
      usually categorized as food, body products or tissues, or environmental material.
      This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).
    title: sample type
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000998
    multivalued: false
    alias: samp_type
    owner: food-food production facility MISAG
    domain_of:
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - food-food production facility
    - food-farm environment
    range: string
    required: true
  samp_stor_media:
    name: samp_stor_media
    description: The liquid that is added to the sample collection device prior to
      sampling. If the sample is pre-hydrated, indicate the liquid media the sample
      is pre-hydrated with for storage purposes. This field accepts terms listed under
      microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067).
      If the proper descriptor is not listed please use text to describe the sample
      storage media.
    title: sample storage media
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001229
    multivalued: false
    alias: samp_stor_media
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: true
  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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001228
    multivalued: false
    alias: samp_stor_device
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: 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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001184
    multivalued: true
    alias: food_product_type
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: true
  IFSAC_category:
    name: IFSAC_category
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001179
    multivalued: true
    alias: IFSAC_category
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: true
  food_product_qual:
    name: food_product_qual
    description: Descriptors for describing food visually or via other senses, which
      is useful for tasks like food inspection where little prior knowledge of how
      the food came to be is available. Some terms like "food (frozen)" are both a
      quality descriptor and the output of a process. This field accepts terms listed
      under food product by quality (http://purl.obolibrary.org/obo/FOODON_00002454).
    title: food product by quality
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001213
    multivalued: false
    alias: food_product_qual
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: true
  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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001131
    multivalued: true
    alias: food_contact_surf
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: true
  facility_type:
    name: facility_type
    description: Establishment details about the type of facility where the sample
      was taken. This is independent of the specific product(s) within the facility.
    title: facility type
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001252
    multivalued: true
    alias: facility_type
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    range: facility_type_enum
    required: 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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001137
    multivalued: true
    alias: food_trav_mode
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  food_trav_vehic:
    name: food_trav_vehic
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001138
    multivalued: true
    alias: food_trav_vehic
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  samp_transport_dur:
    name: samp_transport_dur
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001231
    multivalued: false
    alias: samp_transport_dur
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: quantity value
    required: false
  samp_transport_temp:
    name: samp_transport_temp
    description: Temperature at which sample was transported, e.g. -20 or 4 degree
      Celsius.
    title: sample transport temperature
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{float} {unit} {text}'
    slot_uri: MIXS:0001232
    multivalued: false
    alias: samp_transport_temp
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: false
  samp_collect_method:
    name: samp_collect_method
    description: The method employed for collecting the sample.
    title: sample collection method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001225
    multivalued: false
    alias: samp_collect_method
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  num_samp_collect:
    name: num_samp_collect
    description: The number of samples collected during the current sampling event.
    title: number of samples collected
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001224
    multivalued: false
    alias: num_samp_collect
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    range: quantity value
    required: false
  lot_number:
    name: lot_number
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{integer}, {text}'
    slot_uri: MIXS:0001147
    multivalued: true
    alias: lot_number
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  hygienic_area:
    name: hygienic_area
    description: The subdivision of areas within a food production facility according
      to hygienic requirements. This field accepts terms listed under hygienic food
      production area (http://purl.obolibrary.org/obo/ENVO). Please add a term that
      most accurately indicates the hygienic area your sample was taken from according
      to the definitions provided.
    title: hygienic food production area
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001253
    multivalued: false
    alias: hygienic_area
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    range: string
    required: false
  env_monitoring_zone:
    name: env_monitoring_zone
    description: An environmental monitoring zone is a formal designation as part
      of an environmental monitoring program, in which areas of a food production
      facility are categorized, commonly as zones 1-4, based on likelihood or risk
      of foodborne pathogen contamination. This field accepts terms listed under food
      production environmental monitoring zone (http://purl.obolibrary.org/obo/ENVO).
      Please add a term to indicate the environmental monitoring zone the sample was
      taken from.
    title: food production environmental monitoring zone
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001254
    multivalued: false
    alias: env_monitoring_zone
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    range: string
    required: false
  area_samp_size:
    name: area_samp_size
    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
      sample collected.
    title: area sampled size
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{integer} {unit} x {integer} {unit}'
    slot_uri: MIXS:0001255
    multivalued: false
    alias: area_samp_size
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    range: string
    required: false
  samp_surf_moisture:
    name: samp_surf_moisture
    description: Degree of water held on a sampled surface.  If present, user can
      state the degree of water held on surface (intermittent moisture, submerged).
      If no surface moisture is present indicate not present.
    title: sample surface moisture
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001256
    multivalued: true
    alias: samp_surf_moisture
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    range: samp_surf_moisture_enum
    required: false
  samp_loc_condition:
    name: samp_loc_condition
    description: The condition of the sample location at the time of sampling.
    title: sample location condition
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001257
    multivalued: false
    alias: samp_loc_condition
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    range: samp_loc_condition_enum
    required: false
  biocide_used:
    name: biocide_used
    description: Substance intended for preventing, neutralizing, destroying, repelling,
      or mitigating the effects of any pest or microorganism; that inhibits the growth,
      reproduction, and activity of organisms, including fungal cells; decreases the
      number of fungi or pests present; deters microbial growth and degradation of
      other ingredients in the formulation. Indicate the biocide used on the location
      where the sample was taken. Multiple terms can be separated by pipes.
    title: biocide
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001258
    multivalued: true
    alias: biocide_used
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    range: string
    required: false
  ster_meth_samp_room:
    name: ster_meth_samp_room
    description: The method used to sterilize the sampling room. This field accepts
      terms listed under electromagnetic radiation (http://purl.obolibrary.org/obo/ENVO_01001026).
      If the proper descriptor is not listed, please use text to describe the sampling
      room sterilization method. Multiple terms can be separated by pipes.
    title: sampling room sterilization method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001259
    multivalued: true
    alias: ster_meth_samp_room
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    range: string
    required: 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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001177
    multivalued: false
    alias: enrichment_protocol
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  cult_target:
    name: cult_target
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}|{integer}'
    slot_uri: MIXS:0001119
    multivalued: true
    alias: cult_target
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: 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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001216
    multivalued: false
    alias: microb_cult_med
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: false
  timepoint:
    name: timepoint
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001173
    multivalued: false
    alias: timepoint
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: double
    required: false
  bacterial_density:
    name: bacterial_density
    description: Number of bacteria in sample, as defined by bacteria density (http://purl.obolibrary.org/obo/GENEPIO_0000043).
    title: bacteria density
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001194
    multivalued: false
    alias: bacterial_density
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: quantity value
    required: false
  cult_isol_date:
    name: cult_isol_date
    description: A culture isolation date is a date-time entity 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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001181
    multivalued: false
    alias: cult_isol_date
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: date
    required: 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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001117
    multivalued: false
    alias: cult_result
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: cult_result_enum
    required: false
  cult_result_org:
    name: cult_result_org
    description: Taxonomic information about the cultured organism(s).
    title: culture result organism
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}|{integer}'
    slot_uri: MIXS:0001118
    multivalued: true
    alias: cult_result_org
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: 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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001153
    multivalued: true
    alias: samp_pooling
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  samp_purpose:
    name: samp_purpose
    description: The reason that the sample was collected.
    title: purpose of sampling
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001151
    multivalued: false
    alias: samp_purpose
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: false
  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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001227
    multivalued: false
    alias: samp_rep_tech
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: quantity value
    required: false
  samp_rep_biol:
    name: samp_rep_biol
    description: Measurements of biologically distinct samples that show biological
      variation.
    title: biological sample replicate
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001226
    multivalued: false
    alias: samp_rep_biol
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: quantity value
    required: 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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001230
    multivalued: false
    alias: samp_transport_cont
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: samp_transport_cont_enum
    required: false
  study_design:
    name: study_design
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001236
    multivalued: true
    alias: study_design
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: false
  nucl_acid_ext_kit:
    name: nucl_acid_ext_kit
    description: The name of the extraction kit used to recover the nucleic acid fraction
      of an input material is performed.
    title: nucleic acid extraction kit
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001223
    multivalued: true
    alias: nucl_acid_ext_kit
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    range: string
    required: false
  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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001145
    multivalued: false
    alias: library_prep_kit
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  sequencing_kit:
    name: sequencing_kit
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001155
    multivalued: false
    alias: sequencing_kit
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: 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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001156
    multivalued: false
    alias: sequencing_location
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  study_inc_temp:
    name: study_inc_temp
    description: Sample incubation temperature if unpublished or unvalidated method
      is used.
    title: study incubation temperature
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001238
    multivalued: false
    alias: study_inc_temp
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: quantity value
    required: false
  study_inc_dur:
    name: study_inc_dur
    description: Sample incubation duration if unpublished or unvalidated method is
      used. Indicate the timepoint written in ISO 8601 format.
    title: study incubation duration
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001237
    multivalued: false
    alias: study_inc_dur
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: quantity value
    required: false
  study_timecourse:
    name: study_timecourse
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001239
    multivalued: false
    alias: study_timecourse
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: quantity value
    required: false
  study_tmnt:
    name: study_tmnt
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001240
    multivalued: true
    alias: study_tmnt
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: false
  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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001139
    multivalued: false
    alias: food_source
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: 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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{term}: {term}, {text}'
    slot_uri: MIXS:0001203
    multivalued: true
    alias: food_dis_point
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: false
  food_dis_point_city:
    name: food_dis_point_city
    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)
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001204
    multivalued: false
    alias: food_dis_point_city
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{term}: {term}, {text}'
    slot_uri: MIXS:0001207
    multivalued: false
    alias: food_origin
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: 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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001212
    multivalued: true
    alias: food_prod_synonym
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: false
  food_additive:
    name: food_additive
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001200
    multivalued: true
    alias: food_additive
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: false
  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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001214
    multivalued: false
    alias: food_trace_list
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: food_trace_list_enum
    required: false
  part_plant_animal:
    name: part_plant_animal
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001149
    multivalued: true
    alias: part_plant_animal
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: false
  food_ingredient:
    name: food_ingredient
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001205
    multivalued: true
    alias: food_ingredient
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: false
  spec_intended_cons:
    name: spec_intended_cons
    description: Food consumer type, human or animal, for which the food product is
      produced and marketed. This field accepts terms listed under food consumer group
      (http://purl.obolibrary.org/obo/FOODON_03510136).
    title: specific intended consumer
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001234
    multivalued: true
    alias: spec_intended_cons
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    range: string
    required: 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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001215
    multivalued: true
    alias: HACCP_term
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: false
  dietary_claim_use:
    name: dietary_claim_use
    description: These descriptors are used either for foods intended for special
      dietary use as defined in 21 CFR 105 or for foods that have special characteristics
      indicated in the name or labeling. This field accepts terms listed under dietary
      claim or use (http://purl.obolibrary.org/obo/FOODON_03510023). Multiple terms
      can be separated by one or more pipes, but please consider limiting this list
      to the most prominent dietary claim or use.
    title: dietary claim or use
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001199
    multivalued: true
    alias: dietary_claim_use
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    range: string
    required: false
  food_allergen_label:
    name: food_allergen_label
    description: A label indication that the product contains a recognized allergen.
      This field accepts terms listed under dietary claim or use (http://purl.obolibrary.org/obo/FOODON_03510213).
    title: food allergen labeling
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001201
    multivalued: true
    alias: food_allergen_label
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    range: string
    required: false
  food_prod_char:
    name: food_prod_char
    description: Descriptors of the food production system such as wild caught, free-range,
      organic, free-range, industrial, dairy, beef.
    title: food production characteristics
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001136
    multivalued: true
    alias: food_prod_char
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    - food-farm environment
    range: string
    required: false
  prod_label_claims:
    name: prod_label_claims
    description: Labeling claims containing descriptors such as wild caught, free-range,
      organic, free-range, industrial, hormone-free, antibiotic free, cage free. Can
      include more than one term, separated by ";"
    title: production labeling claims
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    multivalued: true
    alias: prod_label_claims
    owner: food-food production facility MISAG
    domain_of:
    - food-food production facility
    - food-farm environment
    range: string
    required: false
  food_name_status:
    name: food_name_status
    description: A datum indicating that use of a food product name is regulated in
      some legal jurisdiction. This field accepts terms listed under food product
      name legal status (http://purl.obolibrary.org/obo/FOODON_03530087).
    title: food product name legal status
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001206
    multivalued: false
    alias: food_name_status
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    range: string
    required: false
  food_preserv_proc:
    name: food_preserv_proc
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001135
    multivalued: true
    alias: food_preserv_proc
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: false
  food_cooking_proc:
    name: food_cooking_proc
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001202
    multivalued: true
    alias: food_cooking_proc
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: false
  food_treat_proc:
    name: food_treat_proc
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001140
    multivalued: true
    alias: food_treat_proc
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: false
  food_contain_wrap:
    name: food_contain_wrap
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001132
    multivalued: false
    alias: food_contain_wrap
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: false
  food_pack_capacity:
    name: food_pack_capacity
    description: The maximum number of product units within a package
    title: food package capacity
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001208
    multivalued: false
    alias: food_pack_capacity
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: quantity value
    required: 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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001134
    multivalued: true
    alias: food_pack_medium
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: false
  food_prior_contact:
    name: food_prior_contact
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001210
    multivalued: true
    alias: food_prior_contact
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001211
    multivalued: true
    alias: food_prod
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  food_quality_date:
    name: food_quality_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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001178
    multivalued: false
    alias: food_quality_date
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: false
    pattern: ^(best by|best if used by|freeze by||use by);(19|20)\d\d-(0[1-9]|1[012])-(0[1-9]|[12][0-9]|3[01])$
  repository_name:
    name: repository_name
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001152
    multivalued: true
    alias: repository_name
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: false
  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: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{integer}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001144
    multivalued: true
    alias: intended_consumer
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    range: string
    required: false
  food_pack_integrity:
    name: food_pack_integrity
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001209
    multivalued: true
    alias: food_pack_integrity
    owner: food-food production facility MISAG
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    range: string
    required: false
  misc_param:
    name: misc_param
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    multivalued: true
    alias: misc_param
    owner: food-food production facility MISAG
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - air
    - agriculture
    range: string
    required: false