Combination: Mimag combined with FoodAnimalAndAnimalFeed (MimagFoodAnimalAndAnimalFeed)
MIxS Data that comply with the Mimag checklist and the FoodAnimalAndAnimalFeed Extension
Composition
Mimag [Checklist] + FoodAnimalAndAnimalFeed [Extension]
Terms
| MIXS ID | Name | Cardinality and Range | Description |
|---|---|---|---|
| MIXS:0001107 | samp_name | 1 String |
A local identifier or name that for the material sample used for extracting n... |
| MIXS:0000017 | size_frac | 0..1 String |
Filtering pore size used in sample preparation |
| MIXS:0000043 | lib_screen | 0..1 recommended String |
Specific enrichment or screening methods applied before and/or after creating... |
| MIXS:0000062 | ref_db | 0..1 String |
List of database(s) used for ORF annotation, along with version number and re... |
| MIXS:0000038 | nucl_acid_amp | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... |
| MIXS:0000039 | lib_size | 0..1 recommended Integer |
Total number of clones in the library prepared for the project |
| MIXS:0000005 | contam_screen_input | 0..1 ContamScreenInputEnum |
The type of sequence data used as input |
| MIXS:0000047 | mid | 0..1 recommended String |
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe... |
| MIXS:0000057 | assembly_name | 0..1 recommended String |
Name/version of the assembly provided by the submitter that is used in the ge... |
| MIXS:0000113 | temp | 0..1 recommended String |
Temperature of the sample at the time of sampling |
| MIXS:0000069 | compl_score | 1 String |
Completeness score is typically based on either the fraction of markers found... |
| MIXS:0000067 | trnas | 0..1 String |
The total number of tRNAs identified from the SAG or MAG |
| MIXS:0000080 | mag_cov_software | 0..1 MagCovSoftwareEnum |
Tool(s) used to determine the genome coverage if coverage is used as a binnin... |
| MIXS:0000037 | nucl_acid_ext | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... |
| MIXS:0000001 | samp_size | 0..1 recommended String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... |
| MIXS:0000094 | alt | 0..1 recommended String |
Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... |
| MIXS:0000077 | bin_param | 1 BinParamEnum |
The parameters that have been applied during the extraction of genomes from m... |
| MIXS:0000078 | bin_software | 1 String |
Tool(s) used for the extraction of genomes from metagenomic datasets, where p... |
| MIXS:0000026 | source_mat_id | * recommended String |
A unique identifier assigned to a material sample (as defined by http://rs |
| MIXS:0000111 | samp_vol_we_dna_ext | 0..1 String |
Volume (ml) or mass (g) of total collected sample processed for DNA extractio... |
| MIXS:0000040 | lib_reads_seqd | 0..1 recommended Integer |
Total number of clones sequenced from the library |
| MIXS:0000015 | rel_to_oxygen | 0..1 RelToOxygenEnum |
Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ... |
| MIXS:0000079 | reassembly_bin | 0..1 Boolean |
Has an assembly been performed on a genome bin extracted from a metagenomic a... |
| MIXS:0000074 | decontam_software | 0..1 String |
Tool(s) used in contamination screening |
| MIXS:0000002 | samp_collect_device | 0..1 recommended String |
The device used to collect an environmental sample |
| MIXS:0000060 | number_contig | 0..1 Integer |
Total number of contigs in the cleaned/submitted assembly that makes up a giv... |
| MIXS:0000068 | trna_ext_software | 0..1 String |
Tools used for tRNA identification |
| MIXS:0000041 | lib_layout | 0..1 recommended LibLayoutEnum |
Specify whether to expect single, paired, or other configuration of reads |
| MIXS:0000073 | contam_screen_param | 0..1 String |
Specific parameters used in the decontamination sofware, such as reference da... |
| MIXS:0000056 | assembly_qual | 1 AssemblyQualEnum |
The assembly quality category is based on sets of criteria outlined for each ... |
| MIXS:0000025 | ref_biomaterial | 0..1 String |
Primary publication if isolated before genome publication; otherwise, primary... |
| MIXS:0000092 | project_name | 1 String |
Name of the project within which the sequencing was organized |
| MIXS:0000042 | lib_vector | 0..1 recommended String |
Cloning vector type(s) used in construction of libraries |
| MIXS:0000048 | adapters | 0..1 recommended String |
Adapters provide priming sequences for both amplification and sequencing of t... |
| MIXS:0001321 | neg_cont_type | 0..1 recommended NegContTypeEnum |
The substance or equipment used as a negative control in an investigation |
| MIXS:0000058 | assembly_software | 1 String |
Tool(s) used for assembly, including version number and parameters |
| MIXS:0000053 | tax_ident | 1 TaxIdentEnum |
The phylogenetic marker(s) used to assign an organism name to the SAG or MAG |
| MIXS:0000072 | contam_score | 1 Float |
The contamination score is based on the fraction of single-copy genes that ar... |
| MIXS:0000059 | annot | 0..1 String |
Tool used for annotation, or for cases where annotation was provided by a com... |
| MIXS:0000066 | x16s_recover_software | 0..1 String |
Tools used for 16S rRNA gene extraction |
| MIXS:0000065 | x16s_recover | 0..1 Boolean |
Can a 16S gene be recovered from the submitted SAG or MAG? |
| MIXS:0001322 | pos_cont_type | 0..1 recommended String |
The substance, mixture, product, or apparatus used to verify that a process w... |
| MIXS:0000061 | feat_pred | 0..1 String |
Method used to predict UViGs features such as ORFs, integration site, etc |
| MIXS:0000070 | compl_software | 1 String |
Tools used for completion estimate, i |
| MIXS:0000013 | env_local_scale | 1 String |
Report the entity or entities which are in the sample or specimen s local vic... |
| MIXS:0000016 | samp_mat_process | 0..1 recommended String |
A brief description of any processing applied to the sample during or after r... |
| MIXS:0000063 | sim_search_meth | 0..1 String |
Tool used to compare ORFs with database, along with version and cutoffs used |
| MIXS:0000018 | depth | 0..1 recommended String |
The vertical distance below local surface |
| MIXS:0001225 | samp_collect_method | 0..1 recommended String |
The method employed for collecting the sample |
| MIXS:0000071 | compl_appr | 0..1 ComplApprEnum |
The approach used to determine the completeness of a given genomic assembly, ... |
| MIXS:0000014 | env_medium | 1 String |
Report the environmental material(s) immediately surrounding the sample or sp... |
| MIXS:0001320 | samp_taxon_id | 1 String |
NCBI taxon id of the sample |
| MIXS:0000010 | geo_loc_name | 1 String |
The geographical origin of the sample as defined by the country or sea name f... |
| MIXS:0000011 | collection_date | 1 Datetime |
The time of sampling, either as an instance (single point in time) or interva... |
| MIXS:0000050 | seq_meth | 1 String |
Sequencing machine used |
| MIXS:0000009 | lat_lon | 1 String |
The geographical origin of the sample as defined by latitude and longitude |
| MIXS:0000093 | elev | 0..1 recommended String |
Elevation of the sampling site is its height above a fixed reference point, m... |
| MIXS:0000012 | env_broad_scale | 1 String |
Report the major environmental system the sample or specimen came from |
| MIXS:0000064 | tax_class | 0..1 String |
Method used for taxonomic classification, along with reference database used,... |
| MIXS:0000008 | experimental_factor | * recommended String |
Variable aspects of an experiment design that can be used to describe an expe... |
| MIXS:0000091 | associated_resource | * recommended String |
A related resource that is referenced, cited, or otherwise associated to the ... |
| MIXS:0000090 | sop | * recommended String |
Standard operating procedures used in assembly and/or annotation of genomes, ... |
| MIXS:0000103 | organism_count | * String |
Total cell count of any organism (or group of organisms) per gram, volume or ... |
| MIXS:0001335 | spikein_count | 0..1 String |
Total cell count of any organism (or group of organisms) per gram, volume or ... |
| MIXS:0000110 | samp_store_temp | 0..1 String |
Temperature at which sample was stored, e |
| MIXS:0000116 | samp_store_dur | 0..1 String |
Duration for which the sample was stored |
| MIXS:0000325 | pool_dna_extracts | 0..1 String |
Indicate whether multiple DNA extractions were mixed |
| MIXS:0000755 | samp_store_loc | 0..1 String |
Location at which sample was stored, usually name of a specific freezer/room |
| MIXS:0001230 | samp_transport_cont | 0..1 SampTransportContEnum |
Conatiner in which the sample was stored during transport |
| MIXS:0000754 | perturbation | * String |
Type of perturbation, e |
| MIXS:0001183 | coll_site_geo_feat | 1 String |
Text or terms that describe the geographic feature where the food sample was ... |
| MIXS:0001207 | food_origin | 1 String |
A reference to a place on the Earth, by its name or by its geographical locat... |
| MIXS:0001211 | food_prod | 1..* String |
Descriptors of the food production system or of the agricultural environment ... |
| MIXS:0001184 | food_product_type | 1 String |
A food product type is a class of food products that is differentiated by its... |
| MIXS:0001139 | food_source | 0..1 String |
Type of plant or animal from which the food product or its major ingredient i... |
| MIXS:0001179 | IFSAC_category | 1..* String |
The IFSAC food categorization scheme has five distinct levels to which foods ... |
| MIXS:0001144 | intended_consumer | 1..* String |
Food consumer type, human or animal, for which the food product is produced a... |
| MIXS:0001151 | samp_purpose | 1 String |
The reason that the sample was collected |
| MIXS:0001243 | animal_am | 0..1 String |
The name(s) (generic or brand) of the antimicrobial(s) given to the food anim... |
| MIXS:0001244 | animal_am_dur | 0..1 String |
The duration of time (days) that the antimicrobial was administered to the fo... |
| MIXS:0001245 | animal_am_freq | 0..1 Float |
The frequency per day that the antimicrobial was administered to the food ani... |
| MIXS:0001246 | animal_am_route | 0..1 String |
The route by which the antimicrobial is adminstered into the body of the food... |
| MIXS:0001247 | animal_am_use | 0..1 String |
The prescribed intended use of or the condition treated by the antimicrobial ... |
| MIXS:0001248 | animal_body_cond | 0..1 AnimalBodyCondEnum |
Body condition scoring is a production management tool used to evaluate overa... |
| MIXS:0001130 | animal_diet | * String |
If the isolate is from a food animal, the type of diet eaten by the food anim... |
| MIXS:0001113 | animal_feed_equip | * String |
Description of the feeding equipment used for livestock |
| MIXS:0001129 | animal_group_size | 0..1 Integer |
The number of food animals of the same species that are maintained together a... |
| MIXS:0001180 | animal_housing | * String |
Description of the housing system of the livestock |
| MIXS:0001249 | animal_sex | 0..1 AnimalSexEnum |
The sex and reproductive status of the food animal |
| MIXS:0001194 | bacterial_density | 0..1 String |
Number of bacteria in sample, as defined by bacteria density (http://purl |
| MIXS:0001195 | cons_food_stor_dur | 0..1 String |
The storage duration of the food commodity by the consumer, prior to onset of... |
| MIXS:0001196 | cons_food_stor_temp | 0..1 String |
Temperature at which food commodity was stored by the consumer, prior to onse... |
| MIXS:0001197 | cons_purch_date | 0..1 Datetime |
The date a food product was purchased by consumer |
| MIXS:0001198 | cons_qty_purchased | 0..1 String |
The quantity of food purchased by consumer |
| MIXS:0001181 | cult_isol_date | 0..1 Datetime |
The datetime marking the end of a process in which a sample yields a positive... |
| MIXS:0001117 | cult_result | 0..1 CultResultEnum |
Any result of a bacterial culture experiment reported as a binary assessment ... |
| MIXS:0001118 | cult_result_org | * String |
Taxonomic information about the cultured organism(s) |
| MIXS:0001119 | cult_target | * String |
The target microbial analyte in terms of investigation scope |
| MIXS:0001177 | enrichment_protocol | 0..1 String |
The microbiological workflow or protocol followed to test for the presence or... |
| MIXS:0001200 | food_additive | * String |
A substance or substances added to food to maintain or improve safety and fre... |
| MIXS:0001131 | food_contact_surf | * String |
The specific container or coating materials in direct contact with the food |
| MIXS:0001132 | food_contain_wrap | 0..1 String |
Type of container or wrapping defined by the main container material, the con... |
| MIXS:0001202 | food_cooking_proc | * String |
The transformation of raw food by the application of heat |
| MIXS:0001203 | food_dis_point | * String |
A reference to a place on the Earth, by its name or by its geographical locat... |
| MIXS:0001204 | food_dis_point_city | * String |
A reference to a place on the Earth, by its name or by its geographical locat... |
| MIXS:0001205 | food_ingredient | * String |
In this field, please list individual ingredients for multi-component food [F... |
| MIXS:0001208 | food_pack_capacity | 0..1 String |
The maximum number of product units within a package |
| MIXS:0001209 | food_pack_integrity | * String |
A term label and term id to describe the state of the packing material and te... |
| MIXS:0001134 | food_pack_medium | * String |
The medium in which the food is packed for preservation and handling or the m... |
| MIXS:0001135 | food_preserv_proc | * String |
The methods contributing to the prevention or retardation of microbial, enzym... |
| MIXS:0001210 | food_prior_contact | * String |
The material the food contacted (e |
| MIXS:0001212 | food_prod_synonym | * String |
Other names by which the food product is known by (e |
| MIXS:0001213 | food_product_qual | 0..1 String |
Descriptors for describing food visually or via other senses, which is useful... |
| MIXS:0001178 | food_quality_date | 0..1 String |
The date recommended for the use of the product while at peak quality, this d... |
| MIXS:0001251 | food_source_age | 0..1 String |
The age of the food source host organim |
| MIXS:0001214 | food_trace_list | 0..1 FoodTraceListEnum |
The FDA is proposing to establish additional traceability recordkeeping requi... |
| MIXS:0001137 | food_trav_mode | * String |
A descriptor for the method of movement of food commodity along the food dist... |
| MIXS:0001138 | food_trav_vehic | * String |
A descriptor for the mobile machine which is used to transport food commoditi... |
| MIXS:0001140 | food_treat_proc | * String |
Used to specifically characterize a food product based on the treatment or pr... |
| MIXS:0001215 | HACCP_term | * String |
Hazard Analysis Critical Control Points (HACCP) food safety terms; This field... |
| MIXS:0001145 | library_prep_kit | 0..1 String |
Packaged kits (containing adapters, indexes, enzymes, buffers etc |
| MIXS:0001147 | lot_number | * String |
A distinctive alpha-numeric identification code assigned by the manufacturer ... |
| MIXS:0001216 | microb_cult_med | 0..1 String |
A culture medium used to select for, grow, and maintain prokaryotic microorga... |
| MIXS:0001149 | part_plant_animal | * String |
The anatomical part of the organism being involved in food production or cons... |
| MIXS:0001152 | repository_name | * String |
The name of the institution where the sample or DNA extract is held or "sampl... |
| MIXS:0001153 | samp_pooling | * String |
Physical combination of several instances of like material, e |
| MIXS:0001226 | samp_rep_biol | 0..1 String |
Measurements of biologically distinct samples that show biological variation |
| MIXS:0001227 | samp_rep_tech | 0..1 String |
Repeated measurements of the same sample that show independent measures of th... |
| MIXS:0001154 | samp_source_mat_cat | 0..1 String |
This is the scientific role or category that the subject organism or material... |
| MIXS:0001228 | samp_stor_device | 0..1 String |
The container used to store the sample |
| MIXS:0001229 | samp_stor_media | 0..1 String |
The liquid that is added to the sample collection device prior to sampling |
| MIXS:0001231 | samp_transport_dur | 0..1 String |
The duration of time from when the sample was collected until processed |
| MIXS:0001232 | samp_transport_temp | 0..1 String |
Temperature at which sample was transported, e |
| MIXS:0001155 | sequencing_kit | 0..1 String |
Pre-filled, ready-to-use reagent cartridges |
| MIXS:0001156 | sequencing_location | 0..1 String |
The location the sequencing run was performed |
| MIXS:0001157 | serovar_or_serotype | * String |
A characterization of a cell or microorganism based on the antigenic properti... |
| MIXS:0001235 | spikein_AMR | * String |
Qualitative description of a microbial response to antimicrobial agents |
| MIXS:0001171 | spikein_antibiotic | * String |
Antimicrobials used in research study to assess effects of exposure on microb... |
| MIXS:0001169 | spikein_growth_med | * String |
A liquid or gel containing nutrients, salts, and other factors formulated to ... |
| MIXS:0001172 | spikein_metal | * String |
Heavy metals used in research study to assess effects of exposure on microbio... |
| MIXS:0001167 | spikein_org | * String |
Taxonomic information about the spike-in organism(s) |
| MIXS:0001168 | spikein_serovar | * String |
Taxonomic information about the spike-in organism(s) at the serovar or seroty... |
| MIXS:0001170 | spikein_strain | * String |
Taxonomic information about the spike-in organism(s) at the strain level |
| MIXS:0001236 | study_design | * String |
A plan specification comprised of protocols (which may specify how and what k... |
| MIXS:0001237 | study_inc_dur | 0..1 String |
Sample incubation duration if unpublished or unvalidated method is used |
| MIXS:0001238 | study_inc_temp | 0..1 String |
Sample incubation temperature if unpublished or unvalidated method is used |
| MIXS:0001239 | study_timecourse | 0..1 String |
For time-course research studies involving samples of the food commodity, ind... |
| MIXS:0001240 | study_tmnt | * String |
A process in which the act is intended to modify or alter some other material... |
| MIXS:0001173 | timepoint | 0..1 String |
Time point at which a sample or observation is made or taken from a biomateri... |
| MIXS:0000752 | misc_param | * String |
Any other measurement performed or parameter collected, that is not listed he... |
LinkML Source
Direct
name: MimagFoodAnimalAndAnimalFeed
description: MIxS Data that comply with the Mimag checklist and the FoodAnimalAndAnimalFeed
Extension
title: Mimag combined with FoodAnimalAndAnimalFeed
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: FoodAnimalAndAnimalFeed
mixins:
- Mimag
class_uri: MIXS:0010011_0016019
Induced
name: MimagFoodAnimalAndAnimalFeed
description: MIxS Data that comply with the Mimag checklist and the FoodAnimalAndAnimalFeed
Extension
title: Mimag combined with FoodAnimalAndAnimalFeed
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: FoodAnimalAndAnimalFeed
mixins:
- Mimag
attributes:
samp_name:
name: samp_name
annotations:
Preferred_unit:
tag: Preferred_unit
value: ''
description: A local identifier or name that for the material sample used for
extracting nucleic acids, and subsequent sequencing. It can refer either to
the original material collected or to any derived sub-samples. It can have any
format, but we suggest that you make it concise, unique and consistent within
your lab, and as informative as possible. INSDC requires every sample name from
a single Submitter to be unique. Use of a globally unique identifier for the
field source_mat_id is recommended in addition to sample_name
title: sample name
examples:
- value: ISDsoil1
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- sample
slot_uri: MIXS:0001107
alias: samp_name
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: true
size_frac:
name: size_frac
annotations:
Expected_value:
tag: Expected_value
value: filter size value range
description: Filtering pore size used in sample preparation
title: size fraction selected
examples:
- value: 0-0.22 micrometer
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- fraction
- size
string_serialization: '{float}-{float} {unit}'
slot_uri: MIXS:0000017
alias: size_frac
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
range: string
lib_screen:
name: lib_screen
annotations:
Expected_value:
tag: Expected_value
value: screening strategy name
description: Specific enrichment or screening methods applied before and/or after
creating libraries
title: library screening strategy
examples:
- value: enriched, screened, normalized
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
slot_uri: MIXS:0000043
alias: lib_screen
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
ref_db:
name: ref_db
annotations:
Expected_value:
tag: Expected_value
value: names, versions, and references of databases
description: List of database(s) used for ORF annotation, along with version number
and reference to website or publication
title: reference database(s)
examples:
- value: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017
doi:10.1093/nar/gkw975
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- database
string_serialization: '{database};{version};{reference}'
slot_uri: MIXS:0000062
alias: ref_db
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
nucl_acid_amp:
name: nucl_acid_amp
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the enzymatic amplification (PCR,
TMA, NASBA) of specific nucleic acids
title: nucleic acid amplification
examples:
- value: https://phylogenomics.me/protocols/16s-pcr-protocol/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000038
alias: nucl_acid_amp
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
lib_size:
name: lib_size
description: Total number of clones in the library prepared for the project
title: library size
examples:
- value: '50'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
- size
slot_uri: MIXS:0000039
alias: lib_size
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
recommended: true
contam_screen_input:
name: contam_screen_input
description: The type of sequence data used as input
title: contamination screening input
examples:
- value: contigs
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000005
alias: contam_screen_input
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- Misag
range: ContamScreenInputEnum
mid:
name: mid
description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
used to specifically tag unique samples in a sequencing run. Sequence should
be reported in uppercase letters
title: multiplex identifiers
examples:
- value: GTGAATAT
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- identifier
slot_uri: MIXS:0000047
alias: mid
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
pattern: ^[ACGTRKSYMWBHDVN]+$
structured_pattern:
syntax: ^{ambiguous_nucleotides}$
interpolated: true
partial_match: true
assembly_name:
name: assembly_name
annotations:
Expected_value:
tag: Expected_value
value: name and version of assembly
description: Name/version of the assembly provided by the submitter that is used
in the genome browsers and in the community
title: assembly name
examples:
- value: HuRef, JCVI_ISG_i3_1.0
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
string_serialization: '{text} {text}'
slot_uri: MIXS:0000057
alias: assembly_name
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
temp:
name: temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature of the sample at the time of sampling
title: temperature
examples:
- value: 25 degree Celsius
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- temperature
slot_uri: MIXS:0000113
alias: temp
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
compl_score:
name: compl_score
annotations:
Expected_value:
tag: Expected_value
value: quality;percent completeness
description: 'Completeness score is typically based on either the fraction of
markers found as compared to a database or the percent of a genome found as
compared to a closely related reference genome. High Quality Draft: >90%, Medium
Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated
completeness scores'
title: completeness score
examples:
- value: med;60%
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- score
string_serialization: '[high|med|low];{percentage}'
slot_uri: MIXS:0000069
alias: compl_score
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
required: true
trnas:
name: trnas
annotations:
Expected_value:
tag: Expected_value
value: value from 0-21
description: The total number of tRNAs identified from the SAG or MAG
title: number of standard tRNAs extracted
examples:
- value: '18'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- number
string_serialization: '{integer}'
slot_uri: MIXS:0000067
alias: trnas
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- Misag
- Miuvig
range: string
mag_cov_software:
name: mag_cov_software
description: Tool(s) used to determine the genome coverage if coverage is used
as a binning parameter in the extraction of genomes from metagenomic datasets
title: MAG coverage software
examples:
- value: bbmap
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
slot_uri: MIXS:0000080
alias: mag_cov_software
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- Miuvig
range: MagCovSoftwareEnum
nucl_acid_ext:
name: nucl_acid_ext
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the material separation to recover
the nucleic acid fraction from a sample
title: nucleic acid extraction
examples:
- value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000037
alias: nucl_acid_ext
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
samp_size:
name: samp_size
description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
sample collected
title: amount or size of sample collected
examples:
- value: 5 liter
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- sample
- size
slot_uri: MIXS:0000001
alias: samp_size
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
alt:
name: alt
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric
balloons and heights of places such as atmospheric layers and clouds. It is
used to measure the height of an object which is above the earth's surface.
In this context, the altitude measurement is the vertical distance between the
earth's surface above sea level and the sampled position in the air
title: altitude
examples:
- value: 100 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000094
alias: alt
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- HostAssociated
- MiscellaneousNaturalOrArtificialEnvironment
- SymbiontAssociated
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
bin_param:
name: bin_param
description: The parameters that have been applied during the extraction of genomes
from metagenomic datasets
title: binning parameters
examples:
- value: coverage
description: was 'coverage and kmer'
- value: kmer
description: was coverage and kmer
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- parameter
slot_uri: MIXS:0000077
alias: bin_param
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- Miuvig
range: BinParamEnum
required: true
bin_software:
name: bin_software
annotations:
Expected_value:
tag: Expected_value
value: names and versions of software(s) used
description: Tool(s) used for the extraction of genomes from metagenomic datasets,
where possible include a product ID (PID) of the tool(s) used
title: binning software
examples:
- value: MetaCluster-TA (RRID:SCR_004599), MaxBin (biotools:maxbin)
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
string_serialization: '{software};{version}{PID}'
slot_uri: MIXS:0000078
alias: bin_software
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- Miuvig
range: string
required: true
source_mat_id:
name: source_mat_id
annotations:
Expected_value:
tag: Expected_value
value: 'for cultures of microorganisms: identifiers for two culture collections;
for other material a unique arbitrary identifer'
description: A unique identifier assigned to a material sample (as defined by
http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
digital record of a material sample) used for extracting nucleic acids, and
subsequent sequencing. The identifier can refer either to the original material
collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
/bio_material, or /culture_collection may or may not share the same value as
the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
sampled tissue with the same identifier. However, the /culture_collection qualifier
may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
would refer to an identifier from some derived culture from which the nucleic
acids were extracted (e.g. xatc123 or ark:/2154/R2)
title: source material identifiers
examples:
- value: MPI012345
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- identifier
- material
- source
slot_uri: MIXS:0000026
alias: source_mat_id
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- SymbiontAssociated
range: string
recommended: true
multivalued: true
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
annotations:
Preferred_unit:
tag: Preferred_unit
value: milliliter, gram, milligram, square centimeter
description: 'Volume (ml) or mass (g) of total collected sample processed for
DNA extraction. Note: total sample collected should be entered under the term
Sample Size (MIXS:0000001)'
title: sample volume or weight for DNA extraction
examples:
- value: 1500 milliliter
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- dna
- sample
- volume
- weight
slot_uri: MIXS:0000111
alias: samp_vol_we_dna_ext
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
lib_reads_seqd:
name: lib_reads_seqd
description: Total number of clones sequenced from the library
title: library reads sequenced
examples:
- value: '20'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
slot_uri: MIXS:0000040
alias: lib_reads_seqd
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
recommended: true
rel_to_oxygen:
name: rel_to_oxygen
description: Is this organism an aerobe, anaerobe? Please note that aerobic and
anaerobic are valid descriptors for microbial environments
title: relationship to oxygen
examples:
- value: aerobe
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- oxygen
- relationship
slot_uri: MIXS:0000015
alias: rel_to_oxygen
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
range: RelToOxygenEnum
reassembly_bin:
name: reassembly_bin
description: Has an assembly been performed on a genome bin extracted from a metagenomic
assembly?
title: reassembly post binning
examples:
- value: 'no'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- post
slot_uri: MIXS:0000079
alias: reassembly_bin
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- Miuvig
range: boolean
decontam_software:
name: decontam_software
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: Tool(s) used in contamination screening
title: decontamination software
examples:
- value: anvi'o
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
string_serialization: '[checkm/refinem|anvi''o|prodege|bbtools:decontaminate.sh|acdc|combination]'
slot_uri: MIXS:0000074
alias: decontam_software
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- Misag
range: string
samp_collect_device:
name: samp_collect_device
annotations:
Expected_value:
tag: Expected_value
value: device name
description: The device used to collect an environmental sample. This field accepts
terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
title: sample collection device
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- device
- sample
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000002
alias: samp_collect_device
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
number_contig:
name: number_contig
description: Total number of contigs in the cleaned/submitted assembly that makes
up a given genome, SAG, MAG, or UViG
title: number of contigs
examples:
- value: '40'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- number
slot_uri: MIXS:0000060
alias: number_contig
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: integer
trna_ext_software:
name: trna_ext_software
description: Tools used for tRNA identification
title: tRNA extraction software
examples:
- value: infernal;v2;default parameters
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
slot_uri: MIXS:0000068
alias: trna_ext_software
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- Misag
- Miuvig
range: string
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
lib_layout:
name: lib_layout
description: Specify whether to expect single, paired, or other configuration
of reads
title: library layout
examples:
- value: paired
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
slot_uri: MIXS:0000041
alias: lib_layout
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: LibLayoutEnum
recommended: true
contam_screen_param:
name: contam_screen_param
annotations:
Expected_value:
tag: Expected_value
value: enumeration;value or name
description: Specific parameters used in the decontamination sofware, such as
reference database, coverage, and kmers. Combinations of these parameters may
also be used, i.e. kmer and coverage, or reference database and kmer
title: contamination screening parameters
examples:
- value: kmer
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- parameter
string_serialization: '[ref db|kmer|coverage|combination];{text|integer}'
slot_uri: MIXS:0000073
alias: contam_screen_param
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- Misag
range: string
assembly_qual:
name: assembly_qual
description: 'The assembly quality category is based on sets of criteria outlined
for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
contiguous sequence per replicon without gaps or ambiguities with a consensus
error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
where gaps span repetitive regions. Presence of the large subunit (LSU) RNA,
small subunit (SSU) and the presence of 5.8S rRNA or 5S rRNA depending on whether
it is a eukaryotic or prokaryotic genome, respectively. Medium Quality Draft:Many
fragments with little to no review of assembly other than reporting of standard
assembly statistics. Low Quality Draft:Many fragments with little to no review
of assembly other than reporting of standard assembly statistics. Assembly statistics
include, but are not limited to total assembly size, number of contigs, contig
N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated,
contiguous sequence per replicon without gaps or ambiguities, with extensive
manual review and editing to annotate putative gene functions and transcriptional
units. High-quality draft genome: One or multiple fragments, totaling 90%
of the expected genome or replicon sequence or predicted complete. Genome fragment(s):
One or multiple fragments, totalling < 90% of the expected genome or replicon
sequence, or for which no genome size could be estimated'
title: assembly quality
examples:
- value: High-quality draft genome
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- quality
slot_uri: MIXS:0000056
alias: assembly_qual
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: AssemblyQualEnum
required: true
ref_biomaterial:
name: ref_biomaterial
description: Primary publication if isolated before genome publication; otherwise,
primary genome report
title: reference for biomaterial
examples:
- value: doi:10.1016/j.syapm.2018.01.009
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000025
alias: ref_biomaterial
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
project_name:
name: project_name
description: Name of the project within which the sequencing was organized
title: project name
examples:
- value: Forest soil metagenome
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- project
slot_uri: MIXS:0000092
alias: project_name
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: true
lib_vector:
name: lib_vector
annotations:
Expected_value:
tag: Expected_value
value: vector
description: Cloning vector type(s) used in construction of libraries
title: library vector
examples:
- value: Bacteriophage P1
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
slot_uri: MIXS:0000042
alias: lib_vector
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
adapters:
name: adapters
description: Adapters provide priming sequences for both amplification and sequencing
of the sample-library fragments. Both adapters should be reported; in uppercase
letters
title: adapters
examples:
- value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000048
alias: adapters
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
structured_pattern:
syntax: ^{adapter_A_DNA_sequence};{adapter_B_DNA_sequence}$
interpolated: true
partial_match: true
neg_cont_type:
name: neg_cont_type
annotations:
Expected_value:
tag: Expected_value
value: enumeration or text
description: The substance or equipment used as a negative control in an investigation
title: negative control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- type
slot_uri: MIXS:0001321
alias: neg_cont_type
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: NegContTypeEnum
recommended: true
assembly_software:
name: assembly_software
description: Tool(s) used for assembly, including version number and parameters
title: assembly software
examples:
- value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
slot_uri: MIXS:0000058
alias: assembly_software
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
tax_ident:
name: tax_ident
description: The phylogenetic marker(s) used to assign an organism name to the
SAG or MAG
title: taxonomic identity marker
examples:
- value: other
description: was other <colon> rpoB gene
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- identifier
- marker
- taxon
slot_uri: MIXS:0000053
alias: tax_ident
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: TaxIdentEnum
required: true
contam_score:
name: contam_score
description: 'The contamination score is based on the fraction of single-copy
genes that are observed more than once in a query genome. The following scores
are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low
Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be
deposited into any of the public databases'
title: contamination score
examples:
- value: '0.01'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- score
slot_uri: MIXS:0000072
alias: contam_score
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- Misag
range: float
required: true
annot:
name: annot
annotations:
Expected_value:
tag: Expected_value
value: name of tool or pipeline used, or annotation source description
description: Tool used for annotation, or for cases where annotation was provided
by a community jamboree or model organism database rather than by a specific
submitter
title: annotation
examples:
- value: prokka
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000059
alias: annot
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
x16s_recover_software:
name: x16s_recover_software
description: Tools used for 16S rRNA gene extraction
title: 16S recovery software
examples:
- value: rambl;v2;default parameters
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- recover
- software
slot_uri: MIXS:0000066
alias: x16s_recover_software
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- Misag
range: string
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
x16s_recover:
name: x16s_recover
description: Can a 16S gene be recovered from the submitted SAG or MAG?
title: 16S recovered
examples:
- value: 'yes'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- recover
slot_uri: MIXS:0000065
alias: x16s_recover
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- Misag
range: boolean
pos_cont_type:
name: pos_cont_type
description: The substance, mixture, product, or apparatus used to verify that
a process which is part of an investigation delivers a true positive
title: positive control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- type
string_serialization: '{term} or {text}'
slot_uri: MIXS:0001322
alias: pos_cont_type
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
recommended: true
feat_pred:
name: feat_pred
description: Method used to predict UViGs features such as ORFs, integration site,
etc
title: feature prediction
examples:
- value: Prodigal;2.6.3;default parameters
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- feature
- predict
slot_uri: MIXS:0000061
alias: feat_pred
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
compl_software:
name: compl_software
annotations:
Expected_value:
tag: Expected_value
value: names and versions of software(s) used
description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
title: completeness software
examples:
- value: checkm
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
string_serialization: '{software};{version}'
slot_uri: MIXS:0000070
alias: compl_software
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
required: true
env_local_scale:
name: env_local_scale
annotations:
Expected_value:
tag: Expected_value
value: Environmental entities having causal influences upon the entity at
time of sampling
description: 'Report the entity or entities which are in the sample or specimen
s local vicinity and which you believe have significant causal influences on
your sample or specimen. We recommend using EnvO terms which are of smaller
spatial grain than your entry for env_broad_scale. Terms, such as anatomical
sites, from other OBO Library ontologies which interoperate with EnvO (e.g.
UBERON) are accepted in this field. EnvO documentation about how to use the
field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
title: local environmental context
examples:
- value: hillside [ENVO:01000333]
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- context
- environmental
slot_uri: MIXS:0000013
alias: env_local_scale
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
samp_mat_process:
name: samp_mat_process
description: A brief description of any processing applied to the sample during
or after retrieving the sample from environment, or a link to the relevant protocol(s)
performed
title: sample material processing
examples:
- value: filtering of seawater, storing samples in ethanol
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- material
- process
- sample
slot_uri: MIXS:0000016
alias: samp_mat_process
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
sim_search_meth:
name: sim_search_meth
description: Tool used to compare ORFs with database, along with version and cutoffs
used
title: similarity search method
examples:
- value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- method
slot_uri: MIXS:0000063
alias: sim_search_meth
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
depth:
name: depth
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: The vertical distance below local surface. For sediment or soil samples
depth is measured from sediment or soil surface, respectively. Depth can be
reported as an interval for subsurface samples
title: depth
examples:
- value: 10 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- depth
slot_uri: MIXS:0000018
alias: depth
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
samp_collect_method:
name: samp_collect_method
description: The method employed for collecting the sample
title: sample collection method
examples:
- value: swabbing
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- method
- sample
slot_uri: MIXS:0001225
alias: samp_collect_method
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}|{text}$
interpolated: true
partial_match: true
compl_appr:
name: compl_appr
annotations:
Expected_value:
tag: Expected_value
value: text
description: The approach used to determine the completeness of a given genomic
assembly, which would typically make use of a set of conserved marker genes
or a closely related reference genome. For UViG completeness, include reference
genome or group used, and contig feature suggesting a complete genome
title: completeness approach
examples:
- value: other
description: was other <colon> UViG length compared to the average length of
reference genomes from the P22virus genus (NCBI RefSeq v83)
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000071
alias: compl_appr
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Mimag
- Misag
- Miuvig
range: ComplApprEnum
env_medium:
name: env_medium
description: 'Report the environmental material(s) immediately surrounding the
sample or specimen at the time of sampling. We recommend using subclasses of
''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
. Terms from other OBO ontologies are permissible as long as they reference
mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
(e.g. a tree, a leaf, a table top)'
title: environmental medium
examples:
- value: bluegrass field soil [ENVO:00005789]
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- environmental
slot_uri: MIXS:0000014
alias: env_medium
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
samp_taxon_id:
name: samp_taxon_id
description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa
sample. Use 'synthetic metagenome for mock community/positive controls, or
'blank sample' for negative controls
title: taxonomy ID of DNA sample
examples:
- value: Gut Metagenome [NCBITaxon:749906]
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- dna
- identifier
- sample
- taxon
slot_uri: MIXS:0001320
alias: samp_taxon_id
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$
structured_pattern:
syntax: ^{text} \[{NCBItaxon_id}\]$
interpolated: true
partial_match: true
geo_loc_name:
name: geo_loc_name
description: The geographical origin of the sample as defined by the country or
sea name followed by specific region name. Country or sea names should be chosen
from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
(http://purl.bioontology.org/ontology/GAZ)
title: geographic location (country and/or sea,region)
examples:
- value: 'USA: Maryland, Bethesda'
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- geographic
- location
slot_uri: MIXS:0000010
alias: geo_loc_name
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: string
required: true
pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
structured_pattern:
syntax: '^{text}: {text}, {text}$'
interpolated: true
partial_match: true
collection_date:
name: collection_date
description: 'The time of sampling, either as an instance (single point in time)
or interval. In case no exact time is available, the date/time can be right
truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
title: collection date
examples:
- value: '2013-03-25T12:42:31+01:00'
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- date
slot_uri: MIXS:0000011
alias: collection_date
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: datetime
required: true
seq_meth:
name: seq_meth
description: Sequencing machine used. Where possible the term should be taken
from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)
title: sequencing method
examples:
- value: 454 Genome Sequencer FLX [OBI:0000702]
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- method
slot_uri: MIXS:0000050
alias: seq_meth
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
structured_pattern:
syntax: ^{text}|({termLabel} \[{termID}\])$
interpolated: true
partial_match: true
lat_lon:
name: lat_lon
description: The geographical origin of the sample as defined by latitude and
longitude. The values should be reported in decimal degrees, limited to 8 decimal
points, and in WGS84 system
title: geographic location (latitude and longitude)
examples:
- value: 50.586825 6.408977
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- geographic
- location
slot_uri: MIXS:0000009
alias: lat_lon
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: string
required: true
pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$
structured_pattern:
syntax: ^{lat} {lon}$
interpolated: true
partial_match: true
elev:
name: elev
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: Elevation of the sampling site is its height above a fixed reference
point, most commonly the mean sea level. Elevation is mainly used when referring
to points on the earth's surface, while altitude is used for points above the
surface, such as an aircraft in flight or a spacecraft in orbit
title: elevation
examples:
- value: 100 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- elevation
slot_uri: MIXS:0000093
alias: elev
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- HostAssociated
- HydrocarbonResourcesCores
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- Water
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
env_broad_scale:
name: env_broad_scale
description: 'Report the major environmental system the sample or specimen came
from. The system(s) identified should have a coarse spatial grain, to provide
the general environmental context of where the sampling was done (e.g. in the
desert or a rainforest). We recommend using subclasses of EnvO s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.
EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
title: broad-scale environmental context
examples:
- value: rangeland biome [ENVO:01000247]
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- context
- environmental
slot_uri: MIXS:0000012
alias: env_broad_scale
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
tax_class:
name: tax_class
description: Method used for taxonomic classification, along with reference database
used, classification rank, and thresholds used to classify new genomes
title: taxonomic classification
examples:
- value: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification,
default parameters)
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- classification
- taxon
slot_uri: MIXS:0000064
alias: tax_class
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
experimental_factor:
name: experimental_factor
annotations:
Expected_value:
tag: Expected_value
value: text or EFO and/or OBI
description: Variable aspects of an experiment design that can be used to describe
an experiment, or set of experiments, in an increasingly detailed manner. This
field accepts ontology terms from Experimental Factor Ontology (EFO) and/or
Ontology for Biomedical Investigations (OBI)
title: experimental factor
examples:
- value: time series design [EFO:0001779]
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- experimental
- factor
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000008
alias: experimental_factor
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
multivalued: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
associated_resource:
name: associated_resource
annotations:
Expected_value:
tag: Expected_value
value: reference to resource
description: A related resource that is referenced, cited, or otherwise associated
to the sequence
title: relevant electronic resources
examples:
- value: http://www.earthmicrobiome.org/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- resource
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000091
alias: associated_resource
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
multivalued: true
sop:
name: sop
annotations:
Expected_value:
tag: Expected_value
value: reference to SOP
description: Standard operating procedures used in assembly and/or annotation
of genomes, metagenomes or environmental sequences
title: relevant standard operating procedures
examples:
- value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- procedures
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000090
alias: sop
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
multivalued: true
organism_count:
name: organism_count
annotations:
Expected_value:
tag: Expected_value
value: organism name;measurement value;enumeration
description: 'Total cell count of any organism (or group of organisms) per gram,
volume or area of sample, should include name of organism followed by count.
The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
title: organism count
examples:
- value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR
from_schema: https://w3id.org/mixs
keywords:
- count
- organism
string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
slot_uri: MIXS:0000103
alias: organism_count
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
multivalued: true
spikein_count:
name: spikein_count
annotations:
Expected_value:
tag: Expected_value
value: organism name;measurement value;enumeration
Preferred_unit:
tag: Preferred_unit
value: colony forming units per milliliter; colony forming units per gram
of dry weight
description: 'Total cell count of any organism (or group of organisms) per gram,
volume or area of sample, should include name of organism followed by count.
The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) should
also be provided (example: total prokaryotes; 3.5e7 cells per ml; qPCR)'
title: spike-in organism count
examples:
- value: total prokaryotes;3.5e7 colony forming units per milliliter;qPCR
from_schema: https://w3id.org/mixs
keywords:
- count
- organism
- spike
string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
slot_uri: MIXS:0001335
alias: spikein_count
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
range: string
samp_store_temp:
name: samp_store_temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature at which sample was stored, e.g. -80 degree Celsius
title: sample storage temperature
examples:
- value: -80 degree Celsius
from_schema: https://w3id.org/mixs
keywords:
- sample
- storage
- temperature
slot_uri: MIXS:0000110
alias: samp_store_temp
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
samp_store_dur:
name: samp_store_dur
description: Duration for which the sample was stored. Indicate the duration for
which the sample was stored written in ISO 8601 format
title: sample storage duration
examples:
- value: P1Y6M
from_schema: https://w3id.org/mixs
keywords:
- duration
- period
- sample
- storage
slot_uri: MIXS:0000116
alias: samp_store_dur
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
structured_pattern:
syntax: ^{duration}$
interpolated: true
partial_match: true
pool_dna_extracts:
name: pool_dna_extracts
annotations:
Expected_value:
tag: Expected_value
value: pooling status;number of pooled extracts
Preferred_unit:
tag: Preferred_unit
value: gram, milliliter, microliter
description: Indicate whether multiple DNA extractions were mixed. If the answer
yes, the number of extracts that were pooled should be given
title: pooling of DNA extracts (if done)
examples:
- value: yes, 5
from_schema: https://w3id.org/mixs
keywords:
- dna
- pooling
string_serialization: '{boolean},{integer}'
slot_uri: MIXS:0000325
alias: pool_dna_extracts
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
- Soil
range: string
samp_store_loc:
name: samp_store_loc
annotations:
Expected_value:
tag: Expected_value
value: location name
description: Location at which sample was stored, usually name of a specific freezer/room
title: sample storage location
examples:
- value: Freezer no:5
from_schema: https://w3id.org/mixs
keywords:
- location
- sample
- storage
slot_uri: MIXS:0000755
alias: samp_store_loc
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
samp_transport_cont:
name: samp_transport_cont
description: Conatiner in which the sample was stored during transport. Indicate
the location name
title: sample transport container
examples:
- value: cooler
from_schema: https://w3id.org/mixs
keywords:
- sample
- transport
slot_uri: MIXS:0001230
alias: samp_transport_cont
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: SampTransportContEnum
perturbation:
name: perturbation
annotations:
Expected_value:
tag: Expected_value
value: perturbation type name;perturbation interval and duration
description: Type of perturbation, e.g. chemical administration, physical disturbance,
etc., coupled with perturbation regimen including how many times the perturbation
was repeated, how long each perturbation lasted, and the start and end time
of the entire perturbation period; can include multiple perturbation types
title: perturbation
examples:
- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- perturbation
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000754
alias: perturbation
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
multivalued: true
coll_site_geo_feat:
name: coll_site_geo_feat
annotations:
Expected_value:
tag: Expected_value
value: ENVO:00000002 or ENVO:00000070
description: 'Text or terms that describe the geographic feature where the food
sample was obtained by the researcher. This field accepts selected terms listed
under the following ontologies: anthropogenic geographic feature (http://purl.obolibrary.org/obo/ENVO_00000002),
for example agricultural fairground [ENVO:01000986]; garden [ENVO:00000011}
or any of its subclasses; market [ENVO:01000987]; water well [ENVO:01000002];
or human construction (http://purl.obolibrary.org/obo/ENVO_00000070)'
title: collection site geographic feature
examples:
- value: farm [ENVO:00000078]
from_schema: https://w3id.org/mixs
keywords:
- feature
- geographic
- site
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001183
alias: coll_site_geo_feat
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
food_origin:
name: food_origin
description: A reference to a place on the Earth, by its name or by its geographical
location that describes the origin of the food commodity, either in terms of
its cultivation or production. This field accepts terms listed under geographic
location (http://purl.obolibrary.org/obo/GAZ_00000448)
title: food product origin geographic location
examples:
- value: 'USA: Delmarva, Peninsula'
from_schema: https://w3id.org/mixs
keywords:
- food
- geographic
- location
- product
slot_uri: MIXS:0001207
alias: food_origin
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
structured_pattern:
syntax: '^{text}: {text}, {text}$'
interpolated: true
partial_match: true
food_prod:
name: food_prod
description: Descriptors of the food production system or of the agricultural
environment and growing conditions related to the farm production system, such
as wild caught, organic, free-range, industrial, dairy, beef, domestic or cultivated
food production. This field accepts terms listed under food production (http://purl.obolibrary.org/obo/FOODON_03530206).
Multiple terms may apply and can be separated by pipes
title: food production system characteristics
examples:
- value: organic plant cultivation [FOODON:03530253]
from_schema: https://w3id.org/mixs
keywords:
- food
- production
slot_uri: MIXS:0001211
alias: food_prod
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
multivalued: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
food_product_type:
name: food_product_type
annotations:
Expected_value:
tag: Expected_value
value: FOODON:00001002 or FOODON:03309997
description: A food product type is a class of food products that is differentiated
by its food composition (e.g., single- or multi-ingredient), processing and/or
consumption characteristics. This does not include brand name products but it
may include generic food dish categories. This field accepts terms under food
product type (http://purl.obolibrary.org/obo/FOODON:03400361). For terms related
to food product for an animal, consult food product for animal (http://purl.obolibrary.org/obo/FOODON_03309997).
If the proper descriptor is not listed please use text to describe the food
type. Multiple terms can be separated by one or more pipes
title: food product type
examples:
- value: shrimp (peeled, deep-frozen) [FOODON:03317171]
from_schema: https://w3id.org/mixs
keywords:
- food
- product
- type
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001184
alias: food_product_type
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
food_source:
name: food_source
annotations:
Expected_value:
tag: Expected_value
value: FOODON term
description: Type of plant or animal from which the food product or its major
ingredient is derived or a chemical food source [FDA CFSAN 1995]
title: food source
examples:
- value: giant tiger prawn [FOODON:03412612]
from_schema: https://w3id.org/mixs
keywords:
- food
- source
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0001139
alias: food_source
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
IFSAC_category:
name: IFSAC_category
annotations:
Expected_value:
tag: Expected_value
value: IFSAC term
description: 'The IFSAC food categorization scheme has five distinct levels to
which foods can be assigned, depending upon the type of food. First, foods are
assigned to one of four food groups (aquatic animals, land animals, plants,
and other). Food groups include increasingly specific food categories; dairy,
eggs, meat and poultry, and game are in the land animal food group, and the
category meat and poultry is further subdivided into more specific categories
of meat (beef, pork, other meat) and poultry (chicken, turkey, other poultry).
Finally, foods are differentiated by differences in food processing (such as
pasteurized fluid dairy products, unpasteurized fluid dairy products, pasteurized
solid and semi-solid dairy products, and unpasteurized solid and semi-solid
dairy products. An IFSAC food category chart is available from https://www.cdc.gov/foodsafety/ifsac/projects/food-categorization-scheme.html
PMID: 28926300'
title: Interagency Food Safety Analytics Collaboration (IFSAC) category
examples:
- value: Plants:Produce:Vegetables:Herbs:Dried Herbs
from_schema: https://w3id.org/mixs
keywords:
- food
slot_uri: MIXS:0001179
alias: IFSAC_category
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
multivalued: true
intended_consumer:
name: intended_consumer
annotations:
Expected_value:
tag: Expected_value
value: FOODON_03510136 or NCBI taxid
description: Food consumer type, human or animal, for which the food product is
produced and marketed. This field accepts terms listed under food consumer group
(http://purl.obolibrary.org/obo/FOODON_03510136) or NCBI taxid
title: intended consumer
examples:
- value: 9606 o rsenior as food consumer [FOODON:03510254]
from_schema: https://w3id.org/mixs
keywords:
- consumer
string_serialization: '{integer}|{termLabel} [{termID}]'
slot_uri: MIXS:0001144
alias: intended_consumer
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
multivalued: true
samp_purpose:
name: samp_purpose
annotations:
Expected_value:
tag: Expected_value
value: enumeration or {text}
description: The reason that the sample was collected
title: purpose of sampling
examples:
- value: field trial
from_schema: https://w3id.org/mixs
keywords:
- purpose
string_serialization: '[active surveillance in response to an outbreak|active
surveillance not initiated by an outbreak|clinical trial|cluster investigation|environmental
assessment|farm sample|field trial|for cause|industry internal investigation|market
sample|passive surveillance|population based studies|research|research and development]
or {text}'
slot_uri: MIXS:0001151
alias: samp_purpose
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
animal_am:
name: animal_am
description: The name(s) (generic or brand) of the antimicrobial(s) given to the
food animal within the last 30 days
title: food animal antimicrobial
examples:
- value: tetracycline
from_schema: https://w3id.org/mixs
keywords:
- animal
- antimicrobial
- food
slot_uri: MIXS:0001243
alias: animal_am
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
range: string
animal_am_dur:
name: animal_am_dur
description: The duration of time (days) that the antimicrobial was administered
to the food animal
title: food animal antimicrobial duration
examples:
- value: 3 days
from_schema: https://w3id.org/mixs
keywords:
- animal
- antimicrobial
- duration
- food
- period
slot_uri: MIXS:0001244
alias: animal_am_dur
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
range: string
structured_pattern:
syntax: ^{float} days$
interpolated: true
partial_match: true
animal_am_freq:
name: animal_am_freq
description: The frequency per day that the antimicrobial was administered to
the food animal
title: food animal antimicrobial frequency
examples:
- value: '1.5'
from_schema: https://w3id.org/mixs
keywords:
- animal
- antimicrobial
- food
- frequency
slot_uri: MIXS:0001245
alias: animal_am_freq
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
range: float
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
animal_am_route:
name: animal_am_route
description: The route by which the antimicrobial is adminstered into the body
of the food animal
title: food animal antimicrobial route of administration
examples:
- value: oral-feed
from_schema: https://w3id.org/mixs
keywords:
- administration
- animal
- antimicrobial
- food
- route
slot_uri: MIXS:0001246
alias: animal_am_route
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
range: string
animal_am_use:
name: animal_am_use
description: The prescribed intended use of or the condition treated by the antimicrobial
given to the food animal by any route of administration
title: food animal antimicrobial intended use
examples:
- value: shipping fever
from_schema: https://w3id.org/mixs
keywords:
- animal
- antimicrobial
- food
- use
slot_uri: MIXS:0001247
alias: animal_am_use
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
range: string
animal_body_cond:
name: animal_body_cond
description: Body condition scoring is a production management tool used to evaluate
overall health and nutritional needs of a food animal. Because there are different
scoring systems, this field is restricted to three categories
title: food animal body condition
examples:
- value: under conditioned
from_schema: https://w3id.org/mixs
keywords:
- animal
- body
- condition
- food
slot_uri: MIXS:0001248
alias: animal_body_cond
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
range: AnimalBodyCondEnum
animal_diet:
name: animal_diet
annotations:
Expected_value:
tag: Expected_value
value: text or FOODON_03309997
description: If the isolate is from a food animal, the type of diet eaten by the
food animal. Please list the main food staple and the setting, if appropriate. For
a list of acceptable animal feed terms or categories, please see http://www.feedipedia.org. Multiple
terms may apply and can be separated by pipes |Food product for animal covers
foods intended for consumption by domesticated animals. Consult http://purl.obolibrary.org/obo/FOODON_03309997.
If the proper descriptor is not listed please use text to describe the food
type. Multiple terms can be separated by one or more pipes. If the proper descriptor
is not listed please use text to describe the food product type
title: food animal source diet
examples:
- value: Hay [FOODON:03301763]
from_schema: https://w3id.org/mixs
keywords:
- animal
- diet
- food
- source
slot_uri: MIXS:0001130
alias: animal_diet
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
range: string
multivalued: true
animal_feed_equip:
name: animal_feed_equip
annotations:
Expected_value:
tag: Expected_value
value: EOL:0001757
description: Description of the feeding equipment used for livestock. This field
accepts terms listed under feed delivery (http://opendata.inra.fr/EOL/EOL_0001757).
Multiple terms can be separated by pipes
title: animal feeding equipment
examples:
- value: self feeding [EOL:0001645]| straight feed trough [EOL:0001661]
from_schema: https://w3id.org/mixs
keywords:
- animal
- equipment
slot_uri: MIXS:0001113
alias: animal_feed_equip
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
range: string
multivalued: true
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
animal_group_size:
name: animal_group_size
description: The number of food animals of the same species that are maintained
together as a unit, i.e. a herd or flock
title: food animal group size
examples:
- value: '80'
from_schema: https://w3id.org/mixs
keywords:
- animal
- food
- size
slot_uri: MIXS:0001129
alias: animal_group_size
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
range: integer
animal_housing:
name: animal_housing
description: Description of the housing system of the livestock. This field accepts
terms listed under terrestrial management housing system (http://opendata.inra.fr/EOL/EOL_0001605)
title: animal housing system
examples:
- value: pen rearing system [EOL:0001636]
from_schema: https://w3id.org/mixs
keywords:
- animal
slot_uri: MIXS:0001180
alias: animal_housing
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
range: string
multivalued: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
animal_sex:
name: animal_sex
description: The sex and reproductive status of the food animal
title: food animal source sex category
examples:
- value: castrated male
from_schema: https://w3id.org/mixs
keywords:
- animal
- food
- source
slot_uri: MIXS:0001249
alias: animal_sex
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
range: AnimalSexEnum
bacterial_density:
name: bacterial_density
annotations:
Preferred_unit:
tag: Preferred_unit
value: colony forming units per milliliter; colony forming units per gram
of dry weight
description: Number of bacteria in sample, as defined by bacteria density (http://purl.obolibrary.org/obo/GENEPIO_0000043)
title: bacteria density
examples:
- value: 10 colony forming units per gram dry weight
from_schema: https://w3id.org/mixs
keywords:
- density
slot_uri: MIXS:0001194
alias: bacterial_density
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
cons_food_stor_dur:
name: cons_food_stor_dur
annotations:
Preferred_unit:
tag: Preferred_unit
value: hours or days
description: The storage duration of the food commodity by the consumer, prior
to onset of illness or sample collection. Indicate the timepoint written in
ISO 8601 format
title: food stored by consumer (storage duration)
examples:
- value: P5D
from_schema: https://w3id.org/mixs
keywords:
- consumer
- duration)
- food
- storage
slot_uri: MIXS:0001195
alias: cons_food_stor_dur
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodHumanFoods
range: string
pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
structured_pattern:
syntax: ^{duration}$
interpolated: true
partial_match: true
cons_food_stor_temp:
name: cons_food_stor_temp
annotations:
Expected_value:
tag: Expected_value
value: text or measurement value
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature at which food commodity was stored by the consumer, prior
to onset of illness or sample collection
title: food stored by consumer (storage temperature)
examples:
- value: 4 degree Celsius
from_schema: https://w3id.org/mixs
keywords:
- consumer
- food
- storage
- temperature
string_serialization: '{float} {unit}|{text}'
slot_uri: MIXS:0001196
alias: cons_food_stor_temp
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodHumanFoods
range: string
cons_purch_date:
name: cons_purch_date
description: The date a food product was purchased by consumer
title: purchase date
examples:
- value: '2013-03-25T12:42:31+01:00'
from_schema: https://w3id.org/mixs
keywords:
- date
slot_uri: MIXS:0001197
alias: cons_purch_date
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodHumanFoods
range: datetime
cons_qty_purchased:
name: cons_qty_purchased
description: The quantity of food purchased by consumer
title: quantity purchased
examples:
- value: 5 cans
from_schema: https://w3id.org/mixs
keywords:
- quantity
slot_uri: MIXS:0001198
alias: cons_qty_purchased
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodHumanFoods
range: string
pattern: ^[1-9][0-9]* ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{integer} {text}$
interpolated: true
partial_match: true
cult_isol_date:
name: cult_isol_date
description: The datetime marking the end of a process in which a sample yields
a positive result for the target microbial analyte(s) in the form of an isolated
colony or colonies
title: culture isolation date
examples:
- value: '2018-05-11T10:00:00+01:00'
from_schema: https://w3id.org/mixs
keywords:
- culture
- date
- isolation
slot_uri: MIXS:0001181
alias: cult_isol_date
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: datetime
cult_result:
name: cult_result
description: Any result of a bacterial culture experiment reported as a binary
assessment such as positive/negative, active/inactive
title: culture result
examples:
- value: positive
from_schema: https://w3id.org/mixs
keywords:
- culture
slot_uri: MIXS:0001117
alias: cult_result
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: CultResultEnum
cult_result_org:
name: cult_result_org
description: Taxonomic information about the cultured organism(s)
title: culture result organism
examples:
- value: Listeria monocytogenes [NCIT:C86502]
from_schema: https://w3id.org/mixs
keywords:
- culture
- organism
slot_uri: MIXS:0001118
alias: cult_result_org
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$
structured_pattern:
syntax: ^({termLabel} \[{termID}\])|{integer}$
interpolated: true
partial_match: true
cult_target:
name: cult_target
annotations:
Expected_value:
tag: Expected_value
value: NCIT:C14250 or NCBI taxid or culture independent
description: The target microbial analyte in terms of investigation scope. This
field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250).
This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy
title: culture target microbial analyte
examples:
- value: Listeria monocytogenes [NCIT:C86502]
from_schema: https://w3id.org/mixs
keywords:
- culture
- microbial
- target
string_serialization: '{termLabel} [{termID}]|{integer}'
slot_uri: MIXS:0001119
alias: cult_target
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
enrichment_protocol:
name: enrichment_protocol
description: The microbiological workflow or protocol followed to test for the
presence or enumeration of the target microbial analyte(s). Please provide a
PubMed or DOI reference for published protocols
title: enrichment protocol
examples:
- value: 'BAM Chapter 4: Enumeration of Escherichia coli and the Coliform Bacteria'
from_schema: https://w3id.org/mixs
keywords:
- enrichment
- protocol
slot_uri: MIXS:0001177
alias: enrichment_protocol
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}|{text}$
interpolated: true
partial_match: true
food_additive:
name: food_additive
annotations:
Expected_value:
tag: Expected_value
value: FOODON:03412972
description: A substance or substances added to food to maintain or improve safety
and freshness, to improve or maintain nutritional value, or improve taste, texture
and appearance. This field accepts terms listed under food additive (http://purl.obolibrary.org/obo/FOODON_03412972).
Multiple terms can be separated by one or more pipes, but please consider limiting
this list to the top 5 ingredients listed in order as on the food label. See
also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors
title: food additive
examples:
- value: xanthan gum [FOODON:03413321]
from_schema: https://w3id.org/mixs
keywords:
- food
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001200
alias: food_additive
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
food_contact_surf:
name: food_contact_surf
annotations:
Expected_value:
tag: Expected_value
value: FOODON:03500010
description: The specific container or coating materials in direct contact with
the food. Multiple values can be assigned. This field accepts terms listed
under food contact surface (http://purl.obolibrary.org/obo/FOODON_03500010)
title: food contact surface
examples:
- value: cellulose acetate [FOODON:03500034]
from_schema: https://w3id.org/mixs
keywords:
- food
- surface
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001131
alias: food_contact_surf
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
food_contain_wrap:
name: food_contain_wrap
annotations:
Expected_value:
tag: Expected_value
value: FOODON:03490100
description: Type of container or wrapping defined by the main container material,
the container form, and the material of the liner lids or ends. Also type of
container or wrapping by form; prefer description by material first, then by
form. This field accepts terms listed under food container or wrapping (http://purl.obolibrary.org/obo/FOODON_03490100)
title: food container or wrapping
examples:
- value: Plastic shrink-pack [FOODON:03490137]
from_schema: https://w3id.org/mixs
keywords:
- food
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001132
alias: food_contain_wrap
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
food_cooking_proc:
name: food_cooking_proc
annotations:
Expected_value:
tag: Expected_value
value: FOODON:03450002
description: The transformation of raw food by the application of heat. This field
accepts terms listed under food cooking (http://purl.obolibrary.org/obo/FOODON_03450002)
title: food cooking process
examples:
- value: food blanching [FOODON:03470175]
from_schema: https://w3id.org/mixs
keywords:
- food
- process
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001202
alias: food_cooking_proc
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
food_dis_point:
name: food_dis_point
description: 'A reference to a place on the Earth, by its name or by its geographical
location that refers to a distribution point along the food chain. This field
accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448).
Reference: Adam Diamond, James Barham. Moving Food Along the Value Chain: Innovations
in Regional Food Distribution. U.S. Dept. of Agriculture, Agricultural Marketing
Service. Washington, DC. March 2012. http://dx.doi.org/10.9752/MS045.03-2012'
title: food distribution point geographic location
examples:
- value: 'USA: Delmarva, Peninsula'
from_schema: https://w3id.org/mixs
keywords:
- food
- geographic
- location
slot_uri: MIXS:0001203
alias: food_dis_point
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
structured_pattern:
syntax: '^{text}: {text}, {text}$'
interpolated: true
partial_match: true
food_dis_point_city:
name: food_dis_point_city
annotations:
Expected_value:
tag: Expected_value
value: GAZ:00000448
description: 'A reference to a place on the Earth, by its name or by its geographical
location that refers to a distribution point along the food chain. This field
accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448).
Reference: Adam Diamond, James Barham. Moving Food Along the Value Chain: Innovations
in Regional Food Distribution. U.S. Dept. of Agriculture, Agricultural Marketing
Service. Washington, DC. March 2012. http://dx.doi.org/10.9752/MS045.03-2012'
title: food distribution point geographic location (city)
examples:
- value: Atlanta[GAZ:00004445]
from_schema: https://w3id.org/mixs
keywords:
- food
- geographic
- location
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001204
alias: food_dis_point_city
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
range: string
multivalued: true
food_ingredient:
name: food_ingredient
annotations:
Expected_value:
tag: Expected_value
value: FOODON
description: In this field, please list individual ingredients for multi-component
food [FOODON:00002501] and simple foods that is not captured in food_type. Please
use terms that are present in FoodOn. Multiple terms can be separated by one
or more pipes |, but please consider limiting this list to the top 5 ingredients
listed in order as on the food label. See also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors
title: food ingredient
examples:
- value: bean (whole) [FOODON:00002753]
from_schema: https://w3id.org/mixs
keywords:
- food
- ingredient
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001205
alias: food_ingredient
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
food_pack_capacity:
name: food_pack_capacity
annotations:
Preferred_unit:
tag: Preferred_unit
value: grams
description: The maximum number of product units within a package
title: food package capacity
examples:
- value: 454 grams
from_schema: https://w3id.org/mixs
keywords:
- food
- package
slot_uri: MIXS:0001208
alias: food_pack_capacity
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
food_pack_integrity:
name: food_pack_integrity
annotations:
Expected_value:
tag: Expected_value
value: FOODON:03530218
description: A term label and term id to describe the state of the packing material
and text to explain the exact condition. This field accepts terms listed under
food packing medium integrity (http://purl.obolibrary.org/obo/FOODON_03530218)
title: food packing medium integrity
examples:
- value: food packing medium compromised [FOODON:00002517]
from_schema: https://w3id.org/mixs
keywords:
- food
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001209
alias: food_pack_integrity
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
food_pack_medium:
name: food_pack_medium
annotations:
Expected_value:
tag: Expected_value
value: FOODON:03480020
description: The medium in which the food is packed for preservation and handling
or the medium surrounding homemade foods, e.g., peaches cooked in sugar syrup.
The packing medium may provide a controlled environment for the food. It may
also serve to improve palatability and consumer appeal. This includes edible
packing media (e.g. fruit juice), gas other than air (e.g. carbon dioxide),
vacuum packed, or packed with aerosol propellant. This field accepts terms under
food packing medium (http://purl.obolibrary.org/obo/FOODON_03480020). Multiple
terms may apply and can be separated by pipes
title: food packing medium
examples:
- value: packed in fruit juice [FOODON:03480039]
from_schema: https://w3id.org/mixs
keywords:
- food
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001134
alias: food_pack_medium
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
food_preserv_proc:
name: food_preserv_proc
annotations:
Expected_value:
tag: Expected_value
value: FOODON:03470107
description: The methods contributing to the prevention or retardation of microbial,
enzymatic or oxidative spoilage and thus to the extension of shelf life. This
field accepts terms listed under food preservation process (http://purl.obolibrary.org/obo/FOODON_03470107)
title: food preservation process
examples:
- value: food slow freezing [FOODON:03470128]
from_schema: https://w3id.org/mixs
keywords:
- food
- process
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001135
alias: food_preserv_proc
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
food_prior_contact:
name: food_prior_contact
annotations:
Expected_value:
tag: Expected_value
value: FOODON:03530077
description: The material the food contacted (e.g., was processed in) prior to
packaging. This field accepts terms listed under material of contact prior to
food packaging (http://purl.obolibrary.org/obo/FOODON_03530077). If the proper
descriptor is not listed please use text to describe the material of contact
prior to food packaging
title: material of contact prior to food packaging
examples:
- value: processed in stainless steel container [FOODON:03530081]
from_schema: https://w3id.org/mixs
keywords:
- food
- material
- prior
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001210
alias: food_prior_contact
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
food_prod_synonym:
name: food_prod_synonym
description: Other names by which the food product is known by (e.g., regional
or non-English names)
title: food product synonym
examples:
- value: pinot gris
from_schema: https://w3id.org/mixs
keywords:
- food
- product
slot_uri: MIXS:0001212
alias: food_prod_synonym
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
food_product_qual:
name: food_product_qual
description: Descriptors for describing food visually or via other senses, which
is useful for tasks like food inspection where little prior knowledge of how
the food came to be is available. Some terms like "food (frozen)" are both a
quality descriptor and the output of a process. This field accepts terms listed
under food product by quality (http://purl.obolibrary.org/obo/FOODON_00002454)
title: food product by quality
examples:
- value: raw [FOODON:03311126]
from_schema: https://w3id.org/mixs
keywords:
- food
- product
- quality
slot_uri: MIXS:0001213
alias: food_product_qual
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
food_quality_date:
name: food_quality_date
annotations:
Expected_value:
tag: Expected_value
value: enumeration, date
description: The date recommended for the use of the product while at peak quality,
this date is not a reflection of safety unless used on infant formula this date
is not a reflection of safety and is typically labeled on a food product as
"best if used by," best by," "use by," or "freeze by."
title: food quality date
examples:
- value: best by 2020-05-24
from_schema: https://w3id.org/mixs
keywords:
- date
- food
- quality
string_serialization: '[best by|best if used by|freeze by|use by]; date'
slot_uri: MIXS:0001178
alias: food_quality_date
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
food_source_age:
name: food_source_age
annotations:
Preferred_unit:
tag: Preferred_unit
value: days
description: The age of the food source host organim. Depending on the type of
host organism, age may be more appropriate to report in days, weeks, or years
title: food source age
comments:
- ISO 8601 period or measurement value?
examples:
- value: 6 months
from_schema: https://w3id.org/mixs
keywords:
- age
- food
- source
slot_uri: MIXS:0001251
alias: food_source_age
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
food_trace_list:
name: food_trace_list
description: The FDA is proposing to establish additional traceability recordkeeping
requirements (beyond what is already required in existing regulations) for persons
who manufacture, process, pack, or hold foods the Agency has designated for
inclusion on the Food Traceability List. The Food Traceability List (FTL) identifies
the foods for which the additional traceability records described in the proposed
rule would be required. The term Food Traceability List (FTL) refers not only
to the foods specifically listed (https://www.fda.gov/media/142303/download),
but also to any foods that contain listed foods as ingredients
title: food traceability list category
examples:
- value: tropical tree fruits
from_schema: https://w3id.org/mixs
keywords:
- food
slot_uri: MIXS:0001214
alias: food_trace_list
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: FoodTraceListEnum
food_trav_mode:
name: food_trav_mode
description: A descriptor for the method of movement of food commodity along the
food distribution system. This field accepts terms listed under travel mode
(http://purl.obolibrary.org/obo/GENEPIO_0001064). If the proper descrptor is
not listed please use text to describe the mode of travel. Multiple terms can
be separated by one or more pipes
title: food shipping transportation method
examples:
- value: train travel [GENEPIO:0001060]
from_schema: https://w3id.org/mixs
keywords:
- food
- method
- transport
slot_uri: MIXS:0001137
alias: food_trav_mode
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
food_trav_vehic:
name: food_trav_vehic
annotations:
Expected_value:
tag: Expected_value
value: ENVO:01000604
description: A descriptor for the mobile machine which is used to transport food
commodities along the food distribution system. This field accepts terms listed
under vehicle (http://purl.obolibrary.org/obo/ENVO_01000604). If the proper
descrptor is not listed please use text to describe the mode of travel. Multiple
terms can be separated by one or more pipes
title: food shipping transportation vehicle
examples:
- value: aircraft [ENVO:01001488]|car [ENVO:01000605]
from_schema: https://w3id.org/mixs
keywords:
- food
- transport
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001138
alias: food_trav_vehic
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
food_treat_proc:
name: food_treat_proc
annotations:
Expected_value:
tag: Expected_value
value: FOODON:03460111
description: Used to specifically characterize a food product based on the treatment
or processes applied to the product or any indexed ingredient. The processes
include adding, substituting or removing components or modifying the food or
component, e.g., through fermentation. Multiple values can be assigned. This
fields accepts terms listed under food treatment process (http://purl.obolibrary.org/obo/FOODON_03460111)
title: food treatment process
examples:
- value: gluten removal process [FOODON:03460750]
from_schema: https://w3id.org/mixs
keywords:
- food
- process
- treatment
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001140
alias: food_treat_proc
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
HACCP_term:
name: HACCP_term
description: Hazard Analysis Critical Control Points (HACCP) food safety terms;
This field accepts terms listed under HACCP guide food safety term (http://purl.obolibrary.org/obo/FOODON_03530221)
title: Hazard Analysis Critical Control Points (HACCP) guide food safety term
examples:
- value: tetrodotoxic poisoning [FOODON:03530249]
from_schema: https://w3id.org/mixs
keywords:
- food
- term
slot_uri: MIXS:0001215
alias: HACCP_term
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
library_prep_kit:
name: library_prep_kit
annotations:
Expected_value:
tag: Expected_value
value: name of library preparation kit
description: Packaged kits (containing adapters, indexes, enzymes, buffers etc.),
tailored for specific sequencing workflows, which allow the simplified preparation
of sequencing-ready libraries for small genomes, amplicons, and plasmids
title: library preparation kit
examples:
- value: Illumina DNA Prep
from_schema: https://w3id.org/mixs
keywords:
- kit
- library
- preparation
slot_uri: MIXS:0001145
alias: library_prep_kit
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
lot_number:
name: lot_number
annotations:
Expected_value:
tag: Expected_value
value: lot number, item
description: 'A distinctive alpha-numeric identification code assigned by the
manufacturer or distributor to a specific quantity of manufactured material
or product within a batch. Synonym: Batch Number. The submitter should provide
lot number of the item followed by the item name for which the lot number was
provided'
title: lot number
examples:
- value: 1239ABC01A, split Cornish hens
from_schema: https://w3id.org/mixs
keywords:
- number
string_serialization: '{integer}, {text}'
slot_uri: MIXS:0001147
alias: lot_number
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
microb_cult_med:
name: microb_cult_med
description: A culture medium used to select for, grow, and maintain prokaryotic
microorganisms. Can be in either liquid (broth) or solidified (e.g. with agar)
forms. This field accepts terms listed under microbiological culture medium
(http://purl.obolibrary.org/obo/MICRO_0000067). If the proper descriptor is
not listed please use text to describe the culture medium
title: microbiological culture medium
examples:
- value: brain heart infusion agar [MICRO:0000566]
from_schema: https://w3id.org/mixs
keywords:
- culture
- microbiological
slot_uri: MIXS:0001216
alias: microb_cult_med
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
structured_pattern:
syntax: ^{text}|({termLabel} \[{termID}\])$
interpolated: true
partial_match: true
part_plant_animal:
name: part_plant_animal
annotations:
Expected_value:
tag: Expected_value
value: FOODON:03420116
description: The anatomical part of the organism being involved in food production
or consumption; e.g., a carrot is the root of the plant (root vegetable). This
field accepts terms listed under part of plant or animal (http://purl.obolibrary.org/obo/FOODON_03420116)
title: part of plant or animal
examples:
- value: chuck [FOODON:03530021]
from_schema: https://w3id.org/mixs
keywords:
- animal
- plant
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001149
alias: part_plant_animal
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
repository_name:
name: repository_name
annotations:
Expected_value:
tag: Expected_value
value: Institution
description: The name of the institution where the sample or DNA extract is held
or "sample not available" if the sample was used in its entirety for analysis
or otherwise not retained
title: repository name
examples:
- value: FDA CFSAN Microbiology Laboratories
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0001152
alias: repository_name
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
samp_pooling:
name: samp_pooling
description: Physical combination of several instances of like material, e.g.
RNA extracted from samples or dishes of cell cultures into one big aliquot of
cells. Please provide a short description of the samples that were pooled
title: sample pooling
examples:
- value: 5uL of extracted genomic DNA from 5 leaves were pooled
from_schema: https://w3id.org/mixs
keywords:
- pooling
- sample
slot_uri: MIXS:0001153
alias: samp_pooling
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
samp_rep_biol:
name: samp_rep_biol
description: Measurements of biologically distinct samples that show biological
variation
title: biological sample replicate
examples:
- value: 6 replicates
from_schema: https://w3id.org/mixs
keywords:
- sample
slot_uri: MIXS:0001226
alias: samp_rep_biol
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
samp_rep_tech:
name: samp_rep_tech
description: Repeated measurements of the same sample that show independent measures
of the noise associated with the equipment and the protocols
title: technical sample replicate
examples:
- value: 10 replicates
from_schema: https://w3id.org/mixs
keywords:
- sample
slot_uri: MIXS:0001227
alias: samp_rep_tech
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
samp_source_mat_cat:
name: samp_source_mat_cat
annotations:
Expected_value:
tag: Expected_value
value: GENEPIO:0001237
description: This is the scientific role or category that the subject organism
or material has with respect to an investigation. This field accepts terms
listed under specimen source material category (http://purl.obolibrary.org/obo/GENEPIO_0001237
or http://purl.obolibrary.org/obo/OBI_0100051)
title: sample source material category
examples:
- value: environmental (swab or sampling) [GENEPIO:0001732]
from_schema: https://w3id.org/mixs
keywords:
- material
- sample
- source
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0001154
alias: samp_source_mat_cat
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
samp_stor_device:
name: samp_stor_device
annotations:
Expected_value:
tag: Expected_value
value: NCIT:C4318
description: The container used to store the sample. This field accepts terms
listed under container (http://purl.obolibrary.org/obo/NCIT_C43186). If the
proper descriptor is not listed please use text to describe the storage device
title: sample storage device
examples:
- value: Whirl Pak sampling bag [GENEPIO:0002122]
from_schema: https://w3id.org/mixs
keywords:
- device
- sample
- storage
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001228
alias: samp_stor_device
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
samp_stor_media:
name: samp_stor_media
description: The liquid that is added to the sample collection device prior to
sampling. If the sample is pre-hydrated, indicate the liquid media the sample
is pre-hydrated with for storage purposes. This field accepts terms listed under
microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067).
If the proper descriptor is not listed please use text to describe the sample
storage media
title: sample storage media
examples:
- value: peptone water medium [MICRO:0000548]
from_schema: https://w3id.org/mixs
keywords:
- sample
- storage
slot_uri: MIXS:0001229
alias: samp_stor_media
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
structured_pattern:
syntax: ^{text}|({termLabel} \[{termID}\])$
interpolated: true
partial_match: true
samp_transport_dur:
name: samp_transport_dur
annotations:
Preferred_unit:
tag: Preferred_unit
value: days
description: The duration of time from when the sample was collected until processed.
Indicate the duration for which the sample was stored written in ISO 8601 format
title: sample transport duration
examples:
- value: P10D
from_schema: https://w3id.org/mixs
keywords:
- duration
- period
- sample
- transport
slot_uri: MIXS:0001231
alias: samp_transport_dur
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
structured_pattern:
syntax: ^{duration}$
interpolated: true
partial_match: true
samp_transport_temp:
name: samp_transport_temp
annotations:
Expected_value:
tag: Expected_value
value: text or measurement value
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature at which sample was transported, e.g. -20 or 4 degree
Celsius
title: sample transport temperature
examples:
- value: 4 degree Celsius
from_schema: https://w3id.org/mixs
keywords:
- sample
- temperature
- transport
string_serialization: '{float} {unit} {text}'
slot_uri: MIXS:0001232
alias: samp_transport_temp
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
sequencing_kit:
name: sequencing_kit
annotations:
Expected_value:
tag: Expected_value
value: name of sequencing kit used
description: Pre-filled, ready-to-use reagent cartridges. Used to produce improved
chemistry, cluster density and read length as well as improve quality (Q) scores.
Reagent components are encoded to interact with the sequencing system to validate
compatibility with user-defined applications. Indicate name of the sequencing
kit
title: sequencing kit
examples:
- value: NextSeq 500/550 High Output Kit v2.5 (75 Cycles)
from_schema: https://w3id.org/mixs
keywords:
- kit
slot_uri: MIXS:0001155
alias: sequencing_kit
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
sequencing_location:
name: sequencing_location
description: The location the sequencing run was performed. Indicate the name
of the lab or core facility where samples were sequenced
title: sequencing location
examples:
- value: University of Maryland Genomics Resource Center
from_schema: https://w3id.org/mixs
keywords:
- location
slot_uri: MIXS:0001156
alias: sequencing_location
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
serovar_or_serotype:
name: serovar_or_serotype
description: A characterization of a cell or microorganism based on the antigenic
properties of the molecules on its surface. Indicate the name of a serovar or
serotype of interest. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250).
This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy
title: serovar or serotype
examples:
- value: Escherichia coli strain O157:H7 [NCIT:C86883]
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0001157
alias: serovar_or_serotype
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
range: string
multivalued: true
pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$
structured_pattern:
syntax: ^({termLabel} \[{termID}\])|{integer}$
interpolated: true
partial_match: true
spikein_AMR:
name: spikein_AMR
annotations:
Expected_value:
tag: Expected_value
value: measurement value ARO:3004299
description: Qualitative description of a microbial response to antimicrobial
agents. Bacteria may be susceptible or resistant to a broad range of antibiotic
drugs or drug classes, with several intermediate states or phases. This field
accepts terms under antimicrobial phenotype (http://purl.obolibrary.org/obo/ARO_3004299)
title: antimicrobial phenotype of spike-in bacteria
examples:
- value: wild type [ARO:3004432]
from_schema: https://w3id.org/mixs
keywords:
- antimicrobial
- spike
string_serialization: '{float} {unit};{termLabel} [{termID}]'
slot_uri: MIXS:0001235
alias: spikein_AMR
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodHumanFoods
range: string
multivalued: true
spikein_antibiotic:
name: spikein_antibiotic
annotations:
Expected_value:
tag: Expected_value
value: drug name; concentration
description: Antimicrobials used in research study to assess effects of exposure
on microbiome of a specific site. Please list antimicrobial, common name and/or
class and concentration used for spike-in
title: spike-in with antibiotics
examples:
- value: Tetracycline at 5 mg/ml
from_schema: https://w3id.org/mixs
keywords:
- spike
string_serialization: '{text} {integer}'
slot_uri: MIXS:0001171
alias: spikein_antibiotic
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
range: string
multivalued: true
spikein_growth_med:
name: spikein_growth_med
description: A liquid or gel containing nutrients, salts, and other factors formulated
to support the growth of microorganisms, cells, or plants (National Cancer Institute
Thesaurus). A growth medium is a culture medium which has the disposition to
encourage growth of particular bacteria to the exclusion of others in the same
growth environment. In this case, list the culture medium used to propagate
the spike-in bacteria during preparation of spike-in inoculum. This field accepts
terms listed under microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067).
If the proper descriptor is not listed please use text to describe the spike
in growth media
title: spike-in growth medium
examples:
- value: LB broth [MCO:0000036]
from_schema: https://w3id.org/mixs
keywords:
- growth
- spike
slot_uri: MIXS:0001169
alias: spikein_growth_med
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
range: string
multivalued: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
structured_pattern:
syntax: ^{text}|({termLabel} \[{termID}\])$
interpolated: true
partial_match: true
spikein_metal:
name: spikein_metal
annotations:
Expected_value:
tag: Expected_value
value: heavy metal name or chemical symbol; concentration
description: Heavy metals used in research study to assess effects of exposure
on microbiome of a specific site. Please list heavy metals and concentration
used for spike-in
title: spike-in with heavy metals
examples:
- value: Cd at 20 ppm
from_schema: https://w3id.org/mixs
keywords:
- heavy
- spike
string_serialization: '{text} {integer}'
slot_uri: MIXS:0001172
alias: spikein_metal
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
range: string
multivalued: true
spikein_org:
name: spikein_org
description: Taxonomic information about the spike-in organism(s). This field
accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This
field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy.
Multiple terms can be separated by pipes
title: spike in organism
examples:
- value: Listeria monocytogenes [NCIT:C86502]|28901
from_schema: https://w3id.org/mixs
keywords:
- organism
- spike
slot_uri: MIXS:0001167
alias: spikein_org
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
range: string
multivalued: true
pattern: ^(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])|[1-9][0-9]*$
structured_pattern:
syntax: ^({termLabel} \[{termID}\])|{integer}$
interpolated: true
partial_match: true
spikein_serovar:
name: spikein_serovar
annotations:
Expected_value:
tag: Expected_value
value: NCIT:C14250 or antigenic formula or serovar name
description: Taxonomic information about the spike-in organism(s) at the serovar
or serotype level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250).
This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy.
Multiple terms can be separated by pipes
title: spike-in bacterial serovar or serotype
examples:
- value: Escherichia coli strain O157:H7 [NCIT:C86883]|83334
from_schema: https://w3id.org/mixs
keywords:
- spike
string_serialization: '{termLabel} [{termID}]|{integer}'
slot_uri: MIXS:0001168
alias: spikein_serovar
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
range: string
multivalued: true
spikein_strain:
name: spikein_strain
annotations:
Expected_value:
tag: Expected_value
value: NCIT:C14250 or NCBI taxid or text
description: Taxonomic information about the spike-in organism(s) at the strain
level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250).
This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy.
Multiple terms can be separated by pipes
title: spike-in microbial strain
examples:
- value: '169963'
from_schema: https://w3id.org/mixs
keywords:
- microbial
- spike
string_serialization: '{termLabel} [{termID}]|{integer}'
slot_uri: MIXS:0001170
alias: spikein_strain
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
range: string
multivalued: true
study_design:
name: study_design
annotations:
Expected_value:
tag: Expected_value
value: OBI:0500000
description: A plan specification comprised of protocols (which may specify how
and what kinds of data will be gathered) that are executed as part of an investigation
and is realized during a study design execution. This field accepts terms under
study design (http://purl.obolibrary.org/obo/OBI_0500000). If the proper descriptor
is not listed please use text to describe the study design. Multiple terms can
be separated by pipes
title: study design
examples:
- value: in vitro design [OBI:0001285]
from_schema: https://w3id.org/mixs
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001236
alias: study_design
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
study_inc_dur:
name: study_inc_dur
annotations:
Preferred_unit:
tag: Preferred_unit
value: hours or days
description: Sample incubation duration if unpublished or unvalidated method is
used. Indicate the timepoint written in ISO 8601 format
title: study incubation duration
examples:
- value: PT24H
from_schema: https://w3id.org/mixs
keywords:
- duration
- incubation
- period
slot_uri: MIXS:0001237
alias: study_inc_dur
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
structured_pattern:
syntax: ^{duration}$
interpolated: true
partial_match: true
study_inc_temp:
name: study_inc_temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Sample incubation temperature if unpublished or unvalidated method
is used
title: study incubation temperature
examples:
- value: 37 degree Celsius
from_schema: https://w3id.org/mixs
keywords:
- incubation
- temperature
slot_uri: MIXS:0001238
alias: study_inc_temp
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
study_timecourse:
name: study_timecourse
annotations:
Preferred_unit:
tag: Preferred_unit
value: dpi
description: For time-course research studies involving samples of the food commodity,
indicate the total duration of the time-course study
title: time-course duration
examples:
- value: 2 days post inoculation
from_schema: https://w3id.org/mixs
keywords:
- duration
- period
- time
slot_uri: MIXS:0001239
alias: study_timecourse
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
study_tmnt:
name: study_tmnt
annotations:
Expected_value:
tag: Expected_value
value: MCO:0000866
description: A process in which the act is intended to modify or alter some other
material entity. From the study design, each treatment is comprised of one
level of one or multiple factors. This field accepts terms listed under treatment
(http://purl.obolibrary.org/obo/MCO_0000866). If the proper descriptor is not
listed please use text to describe the study treatment. Multiple terms can be
separated by one or more pipes
title: study treatment
examples:
- value: Factor A|spike-in|levels high, medium, low
from_schema: https://w3id.org/mixs
keywords:
- treatment
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001240
alias: study_tmnt
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
timepoint:
name: timepoint
annotations:
Preferred_unit:
tag: Preferred_unit
value: hours or days
description: Time point at which a sample or observation is made or taken from
a biomaterial as measured from some reference point. Indicate the timepoint
written in ISO 8601 format
title: timepoint
examples:
- value: PT24H
from_schema: https://w3id.org/mixs
keywords:
- time
slot_uri: MIXS:0001173
alias: timepoint
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
structured_pattern:
syntax: ^{duration}$
interpolated: true
partial_match: true
misc_param:
name: misc_param
annotations:
Expected_value:
tag: Expected_value
value: parameter name;measurement value
description: Any other measurement performed or parameter collected, that is not
listed here
title: miscellaneous parameter
examples:
- value: Bicarbonate ion concentration;2075 micromole per kilogram
from_schema: https://w3id.org/mixs
keywords:
- parameter
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
alias: misc_param
owner: MimagFoodAnimalAndAnimalFeed
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
multivalued: true
class_uri: MIXS:0010011_0016019