Food-animal and animal feed

Mandatory Attributes Optional Attributes

Mandatory Attributes

Collection site geographic feature

• Harmonized name: coll_site_geo_feat

• Description: Text or terms that describe the geographic feature where the food sample was obtained by the researcher. This field encourages 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), e.g., grocery store [GENEPIO:0001020]

Collection date

• Harmonized name: collection_date

• Description: the date on which the sample was collected; date/time ranges are supported by providing two dates from among the supported value formats, delimited by a forward-slash character; collection times are supported by adding "T", then the hour and minute after the date, and must be in Coordinated Universal Time (UTC), otherwise known as "Zulu Time" (Z); supported formats include "DD-Mmm-YYYY", "Mmm-YYYY", "YYYY" or ISO 8601 standard "YYYY-mm-dd", "YYYY-mm", "YYYY-mm-ddThh:mm:ss"; e.g., 30-Oct-1990, Oct-1990, 1990, 1990-10-30, 1990-10, 21-Oct-1952/15-Feb-1953, 2015-10-11T17:53:03Z; valid non-ISO dates will be automatically transformed to ISO format

Broad-scale environmental context

• Harmonized name: env_broad_scale

• Description: Add terms that identify the major environment type(s) where your sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes e.g.: mangrove biome [ENVO:01000181]|estuarine biome [ENVO:01000020]

Local-scale environmental context

• Harmonized name: env_local_scale

• Description: Add terms that identify environmental entities having causal influences upon the entity at time of sampling, multiple terms can be separated by pipes, e.g.: shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316]

Environmental medium

• Harmonized name: env_medium

• Description: Add terms that identify the material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. Multiple terms can be separated by pipes e.g.: estuarine water [ENVO:01000301]|estuarine mud [ENVO:00002160]

Food product origin geographic location

• Harmonized 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 encourages terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448), e.g., Thailand

Food production characteristics

• Harmonized name: food_prod_char

• Description: Descriptors of the food production system such as wild caught, free-range, organic, free-range, industrial, dairy, beef

Food product type

• Harmonized name: food_product_type

• Description: A food product type is a class of food products that is differentiated by its food composition (e.g., single- or multi-ingredient), processing and/or consumption characteristics. This does not include brand name products but it may include generic food dish categories. This field encourages 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, e.g., multi-component food product [FOODON:00002501]

Geographic location

• Harmonized name: geo_loc_name

• Description: Geographical origin of the sample; use the appropriate name from this list https://www.insdc.org/submitting-standards/geo_loc_name-qualifier-vocabulary/. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps"

Interagency Food Safety Analytics Collaboration (IFSAC) category

• Harmonized name: ifsac_category

• Description: The IFSAC food categorization scheme has five distinct levels to which foods can be assigned, depending upon the type of food. First, foods are assigned to one of four food groups (aquatic animals, land animals, plants, and other). Food groups include increasingly specific food categories; dairy, eggs, meat and poultry, and game are in the land animal food group, and the category meat and poultry is further subdivided into more specific categories of meat (beef, pork, other meat) and poultry (chicken, turkey, other poultry). Finally, foods are differentiated by differences in food processing (such as pasteurized fluid dairy products, unpasteurized fluid dairy products, pasteurized solid and semi-solid dairy products, and unpasteurized solid and semi-solid dairy products. An IFSAC food category chart is available from https://www.cdc.gov/foodsafety/ifsac/projects/food-categorization-scheme.html PMID: 28926300, e.g., Plants:Produce:Vegetables:Herbs:Dried Herbs

Intended consumer

• Harmonized name: intended_consumer

• Description: Food consumer type, human or animal, for which the food product is produced and marketed, e.g., human

Latitude and longitude

• Harmonized name: lat_lon

• Description: The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W

Purpose of sampling

• Harmonized name: purpose_of_sampling

• Description: the reason that the sample was collected, e.g., 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

NCBI Taxonomy ID

• Description: NCBI’s taxonomy identifier of the organism for this sample. The NCBI taxonomy ID can be found at https://www.ncbi.nlm.nih.gov/taxonomy/. Enter 32644 (which is a taxonomy ID for unidentified organisms) for the following or similar cases: (1) when NCBI taxonomy ID is not available because NCBI taxonomy does not yet cover the organism, (2) when metagenome or environmental sample was used, whose organismal composition is unknown in advance

• Example: 9606 (for Homo sapiens), 452680 (for Pseudomonas sp. UK4)

Organism

• Description: The most descriptive organism name for this sample (to the species, if possible). In the case of a new species, provide the desired organism name. In the case of unidentified species, choose the appropriate Genus and include ‘sp.’, e.g. “Escherichia sp.”. When sequencing a genome from a non-metagenomic source, include a strain or isolate name too, e.g. “Pseudomonas sp. UK4”

• Example: Homo sapiens, Pseudomonas sp. UK4

Sample name

• Description: A name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every sample name from a single submitter must be unique within a single BioProject

Optional Attributes

Food animal antimicrobial duration

• Harmonized name: animal_am_dur

• Description: The duration of time (days) that the antimicrobial was administered to the food animal

Food animal antimicrobial frequency

• Harmonized name: animal_am_freq

• Description: The frequency per day that the antimicrobial was adminstered to the food animal

Food animal antimicrobial route of administration

• Harmonized name: animal_am_route

• Description: The route by which the antimicrobial is adminstered into the body of the food animal

Food animal antimicrobial intended use

• Harmonized 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

Food animal body condition

• Harmonized 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, e.g., normal, over conditioned, under conditioned

Food animal source diet

• Harmonized name: animal_diet

• 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

Animal feeding equipment

• Harmonized name: animal_feed_equip

• 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 one or more pipes

Food animal source sex category

• Harmonized name: animal_sex

• Description: The sex and reproductive status of the food animal, e.g., castrated female, castrated male, intact female, intact male

Bacterial density

• Harmonized name: bacterial_density

• Description: Number of bacteria in sample, as defined by bacteria density (http://purl.obolibrary.org/obo/GENEPIO_0000043)

Collection method

• Harmonized name: collection_method

• Description: Process used to collect the sample, e.g., bronchoalveolar lavage (BAL)

Food stored by consumer (storage duration)

• Harmonized name: cons_food_stor_dur

• 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

Food stored by consumer (storage temperature)

• Harmonized name: cons_food_stor_temp

• Description: Temperature at which food commodity was stored by the consumer, prior to onset of illness or sample collection

Purchase date

• Harmonized name: cons_purch_date

• Description: The date a food product was purchased by consumer

Quantity purchased

• Harmonized name: cons_qty_purchased

• Description: The quantity of food purchased by consumer

Culture isolation date

• Harmonized name: cult_isol_date

• Description: A culture isolation date is a date-time entity marking the end of a process in which a sample yields a positive result for the target microbial analyte(s) in the form of an isolated colony or colonies, e.g., 5/24/2020

Culture result

• Harmonized name: cult_result

• Description: Any result of a bacterial culture experiment reported as a binary assessment, e.g., absent, active, inactive, negative, no, present, positive, yes

Culture result organism

• Harmonized name: cult_result_org

• Description: Taxonomic information about the cultured organism(s)

Culture target microbial analyte

• Harmonized name: cult_target

• Description: The target microbial analyte in terms of investigation scope. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy

Derived from

• Description: Indicates when one BioSample was derived from another BioSample. Value should include BioSample accession number(s)

• Example: SAMN00000001, KAS24095074

Enrichment protocol

• Harmonized 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

Experimental factor

• Harmonized name: experimental_factor

• Description: Variable aspect of experimental design

Food additive

• Harmonized name: food_additive

• Description: A substance or substances added to food to maintain or improve safety and freshness, to improve or maintain nutritional value, or improve taste, texture and appearance. This field encourages 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, e.g., xanthan gum [FOODON:03413321]

Food contact surface

• Harmonized name: food_contact_surf

• Description: The specific container or coating materials in direct contact with the food. Multiple values can be assigned. This field encourages terms listed under food contact surface (http://purl.obolibrary.org/obo/FOODON_03500010), e.g., aluminum surface [FOODON:03500042]

Food container or wrapping

• Harmonized name: food_contain_wrap

• Description: Type of container or wrapping defined by the main container material, the container form, and the material of the liner lids or ends. Also type of container or wrapping by form; prefer Description: by material first, then by form. This field encourages terms listed under food container or wrapping (http://purl.obolibrary.org/obo/FOODON_03490100), e.g., bottle or jar [FOODON:03490203]

Food cooking process

• Harmonized name: food_cooking_proc

• Description: The transformation of raw food by the application of heat. This field encourages terms listed under food cooking (http://purl.obolibrary.org/obo/FOODON_03450002), e.g., food blanching [FOODON:03470175]

Food distribution point geographic location

• Harmonized 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

Food distribution point geographic location (city)

• Harmonized name: food_dis_point_city

Food ingredient

• Harmonized name: food_ingredient

• Description: In this field, please list individual ingredients for multi-component food [FOODON:00002501] and simple foods that is not captured in food_type. Please use terms that are present in FoodOn. Multiple terms can be separated by one or more pipes, but please consider limiting this list to the top 5 ingredients listed in order as on the food label. See also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors

Food package capacity

• Harmonized name: food_pack_capacity

• Description: The maximum number of product units within a package

Food packing integrity

• Harmonized name: food_pack_integrity

• Description: A term label and term id to describe the state of the packing material and text to explain the exact condition. This field encourages terms listed under food packing medium integrity (http://purl.obolibrary.org/obo/FOODON_03530218), e.g., food packing medium compromised [FOODON:00002517]

Food packing medium

• Harmonized name: food_pack_medium

• Description: The medium in which the food is packed for preservation and handling or the medium surrounding homemade foods, e.g., peaches cooked in sugar syrup. The packing medium may provide a controlled environment for the food. It may also serve to improve palatability and consumer appeal. This includes edible packing media (e.g. fruit juice), gas other than air (e.g. carbon dioxide), vacuum packed, or packed with aerosol propellant. This field encourages terms under food packing medium (http://purl.obolibrary.org/obo/FOODON_03480020). Multiple terms may apply and can be separated by pipes, e.g., vacuum-packed [FOODON:03480027]

Food preservation process

• Harmonized name: food_preserv_proc

• Description: The methods contributing to the prevention or retardation of microbial, enzymatic or oxidative spoilage and thus to the extension of shelf life. This field encourages terms listed under food preservation process (http://purl.obolibrary.org/obo/FOODON_03470107), e.g., food fermentation [FOODON:00001304]

Material of contact prior to food packaging

• Harmonized name: food_prior_contact

• Description: The material the food contacted (e.g., was processed in) prior to packaging. This field accepts terms listed under material of contact prior to food packaging (http://purl.obolibrary.org/obo/FOODON_03530077). If the proper descriptor is not listed please use text to describe the material of contact prior to food packaging

Food product synonym

• Harmonized name: food_prod_synonym

• Description: Other names by which the food product is known by (e.g., regional or non-English names), e.g., pinot gris

Food product by quality

• Harmonized 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)

Food quality date

• Harmonized name: food_quality_date

• Description: The date recommended for the use of the product while at peak quality, this date is not a reflection of safety unless used on infant formula this date is not a reflection of safety and is typically labeled on a food product as ""best if used by,"" best by,"" ""use by,"" or ""freeze by"", e.g., 5/24/2020

Food source

• Harmonized name: food_source

• Description: Individual organism or category of organisms from which the food product or its major ingredient is derived, e.g., giant tiger prawn [FOODON:03412612]

Food source age

• Harmonized name: food_source_age

• 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

Food traceability list category

• Harmonized 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, e.g., tropical tree fruits

Food shipping transportation method

• Harmonized 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

Food shipping transportation vehicle

• Harmonized name: food_trav_vehic

• Description: A descriptor for the mobile machine which is used to transport food commodities along the food distribution system. This field accepts terms listed under vehicle (http://purl.obolibrary.org/obo/ENVO_01000604). If the proper descrptor is not listed please use text to describe the mode of travel. Multiple terms can be separated by one or more pipes

Food treatment process

• Harmonized name: food_treat_proc

• Description: Used to specifically characterize a food product based on the treatment or processes applied to the product or any indexed ingredient. The processes include adding, substituting or removing components or modifying the food or component, e.g., through fermentation. Multiple values can be assigned. This fields accepts terms listed under food treatment process (http://purl.obolibrary.org/obo/FOODON_03460111)

Hazard Analysis Critical Control Points (HACCP) guide food safety term

• Harmonized 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)

Antimicrobial name

• Harmonized name: host_am

• Description: The class(es) or name(s) (generic or brand) of the antimicrobial(s) given to the food animal within the last 30 days, e.g., tetracycline [CHEBI:27902]

Food animal group size

• Harmonized name: host_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, e.g., 80

Animal housing system

• Harmonized name: host_housing

• Description: Description: of the housing system of the livestock. This field encourages terms listed under terrestrial management housing system (http://opendata.inra.fr/EOL/EOL_0001605), e.g., pen [EOL:0001902]

Isolation source

• Harmonized name: isolation_source

• Description: Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.

Lot number

• Harmonized name: lot_number

• Description: A distinctive alpha-numeric identification code assigned by the manufacturer or distributor to a specific quantity of manufactured material or product within a batch. The submitter should provide lot number of the item followed by the item name for which the lot number was provided

Microbiological culture medium

• Harmonized 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

Miscellaneous parameter

• Harmonized name: misc_param

• Description: any other measurement performed or parameter collected, that is not listed here

Negative control type

• Harmonized name: neg_cont_type

• Description: The substance or equipment used as a negative control in an investigation, e.g., distilled water, phosphate buffer, empty collection device, empty collection tube, DNA-free PCR mix, sterile swab, sterile syringe

Omics Observatory ID

• Harmonized name: omics_observ_id

• Description: A unique identifier of the omics-enabled observatory (or comparable time series) your data derives from. This identifier should be provided by the OMICON ontology; if you require a new identifier for your time series, contact the ontology's developers. Information is available here: https://github.com/GLOMICON/omicon. This field is only applicable to records which derive from an omics time-series or observatory.

Organism count

• Harmonized name: organism_count

• Description: total count of any organism per gram or volume of sample,should include name of organism followed by count; can include multiple organism counts

Part of plant or animal

• Harmonized name: part_plant_animal

• Description: The anatomical part of the organism being involved in food production or consumption; e.g., a carrot is the root of the plant (root vegetable). This field accepts terms listed under part of plant or animal (http://purl.obolibrary.org/obo/FOODON_03420116)

Perturbation

• Harmonized name: perturbation

• Description: type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types

Pooling of DNA extracts

• Harmonized name: pool_dna_extracts

• Description: were multiple DNA extractions mixed? how many?

Positive control type

• Harmonized 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

Reference for biomaterial

• Harmonized name: ref_biomaterial

• Description: Primary publication or genome report

Relationship to oxygen

• Harmonized name: rel_to_oxygen

• Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments, eg, aerobe, anaerobe, facultative, microaerophilic, microanaerobe, obligate aerobe, obligate anaerobe, missing, not applicable, not collected, not provided, restricted access

Repository

• Harmonized name: repository

• 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

Sample collection device or method

• Harmonized name: samp_collect_device

• Description: Method or device employed for collecting sample

Sample collection method

• Harmonized name: samp_collect_method

• Description: The method employed for collecting the sample

Sample material processing

• Harmonized name: samp_mat_process

• Description: Processing applied to the sample during or after isolation

Sample pooling

• Harmonized 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

Biological sample replicate

• Harmonized name: samp_rep_biol

• Description: Measurements of biologically distinct samples that show biological variation

Technical sample replicate

• Harmonized 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

Sample size

• Harmonized name: samp_size

• Description: Amount or size of sample (volume, mass or area) that was collected

Sample source material category

• Harmonized name: samp_source_mat_cat

• Description: This is the scientific role or category that the subject organism or material has with respect to an investigation. This field accepts terms listed under specimen source material category (http://purl.obolibrary.org/obo/GENEPIO_0001237 or http://purl.obolibrary.org/obo/OBI_0100051)

Sample storage device

• Harmonized name: samp_stor_device

• Description: The container used to store the sample. This field accepts terms listed under container (http://purl.obolibrary.org/obo/NCIT_C43186). If the proper descriptor is not listed please use text to describe the storage device

Sample storage media

• Harmonized 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

Sample storage duration

• Harmonized name: samp_store_dur

• Description:

Sample storage location

• Harmonized name: samp_store_loc

Sample storage temperature

• Harmonized name: samp_store_temp

Sample transport container

• Harmonized name: samp_transport_cont

• Description: Container in which the sample was stored during transport. Indicate the location name, e.g., bottle, cooler, glass vial, plastic vial, vendor supplied container

Sample transport duration

• Harmonized name: samp_transport_dur

• Description: The duration of time from when the sample was collected until processed. Indicate the duration for which the sample was stored written in ISO 8601 format

Sample transport temperature

• Harmonized name: samp_transport_temp

• Description: Temperature at which sample was transported, e.g., -20 or 4 degree Celsius

Sample volume or weight for DNA extraction

• Harmonized name: samp_vol_we_dna_ext

• Description: volume (mL) or weight (g) of sample processed for DNA extraction

Serovar or serotype

• Harmonized 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

Size fraction selected

• Harmonized name: size_frac

• Description: Filtering pore size used in sample preparation, e.g., 0-0.22 micrometer

Source material identifiers

• Harmonized name: source_material_id

• Description: unique identifier assigned to 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.

Antimicrobial phenotype of spike-in bacteria

• Harmonized name: spikein_amr

• 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)

Spike-in with antibiotics

• Harmonized name: spikein_antibiotic

• 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

Spike-in organism count

• Harmonized name: spikein_count

• Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g., qPCR, atp, mpn, etc.) should also be provided, e.g., total prokaryotes; 3.5e7 cells per ml; qPCR

Spike-in growth medium

• Harmonized 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

Spike-in with heavy metals

• Harmonized name: spikein_metal

• 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

Spike in organism

• Harmonized 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

Spike-in bacterial serovar or serotype

• Harmonized name: spikein_serovar

• 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

Spike-in microbial strain

• Harmonized name: spikein_strain

• 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

Study design

• Harmonized name: study_design

• Description: Epidemiological or omics reseach design context that this biosample was used in.

Study incubation duration

• Harmonized name: study_inc_dur

• Description: Sample incubation duration if unpublished or unvalidated method is used. Indicate the timepoint written in ISO 8601 format

Study incubation temperature

• Harmonized name: study_inc_temp

• Description: Sample incubation temperature if unpublished or unvalidated method is used

Time-course duration

• Harmonized name: study_timecourse

• Description: For time-course research studies involving samples of the food commodity, indicate the total duration of the time-course study

Study treatment

• Harmonized name: study_tmnt

• Description: A process in which the act is intended to modify or alter some other material entity. From the study design, each treatment is comprised of one level of one or multiple factors. This field accepts terms listed under treatment (http://purl.obolibrary.org/obo/MCO_0000866). If the proper descriptor is not listed please use text to describe the study treatment. Multiple terms can be separated by one or more pipes

Temperature

• Harmonized name: temp

• Description: temperature of the sample at time of sampling

Timepoint

• Harmonized name: timepoint

• Description: Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point. Indicate the timepoint written in ISO 8601 format