One Health Enteric; version 1.0 Package

You can download package details in xml format or as an Excel spreadsheet.

Name

Description

Use for microbial samples that are collected for genomic surveillance of enteric pathogens by US Health agencies. Includes the One Health Enteric (https://github.com/CFSAN-Biostatistics/One_Health_Enteric_Package) sample spaces: 1. human/animal hosts; 2. food samples; 3. food facilities; 4. environmental samples (farm, water, and the environment).

Mandatory Attributes

collected by

• Harmonized namecollected_by
• DescriptionName of persons or institute who collected the sample

collection date

• Harmonized namecollection_date
• Descriptionthe 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

geographic location

• Harmonized namegeo_loc_name
• DescriptionGeographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-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"

isolation source

• Harmonized nameisolation_source
• DescriptionDescribes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.

purpose of sampling

• Harmonized namepurpose_of_sampling
• Descriptionthe 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

source type

• Harmonized namesource_type
• DescriptionControlled vocabulary describing the isolation_source. Choose the best fit term: Human, Animal, Food, Environmental, Other, e.g., Food

strain

• Harmonized namestrain
• Descriptionmicrobial or eukaryotic strain name

Optional Attributes

animal environment

• Harmonized nameanimal_env
• DescriptionThe environment from which the animal sample was taken, e.g., veterinary clinic

animal intrusion near sample source

• Harmonized nameanimal_intrusion
• DescriptionIdentification of animals intruding on the sample or sample site including invertebrates (such as pests or pollinators) and vertebrates (such as wildlife or domesticated animals). This field encourages terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also encourages identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes, e.g., large flies

biocide used

• Harmonized namebiocide_used
• DescriptionSubstance intended for preventing, neutralizing, destroying, repelling, or mitigating the effects of any pest or microorganism; that inhibits the growth, reproduction, and activity of organisms, including fungal cells; decreases the number of fungi or pests present; deters microbial growth and degradation of other ingredients in the formulation. Indicate the biocide used on the location where the sample was taken. Multiple terms can be separated by pipes, e.g., Quaternary ammonium compound|SterBac

building setting

• Harmonized namebuilding_setting
• Descriptionlocation (geography) where a building is set

collection site geographic feature

• Harmonized namecoll_site_geo_feat
• DescriptionText 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]

culture isolation date

• Harmonized namecult_isol_date
• DescriptionA 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 collection

• Harmonized nameculture_collection
• DescriptionName of source institute and unique culture identifier. See the description for the proper format and list of allowed institutes, http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier

broad-scale environmental context

• Harmonized nameenv_broad_scale
• DescriptionAdd 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 nameenv_local_scale
• DescriptionAdd 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 nameenv_medium
• DescriptionAdd 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 production environmental monitoring zone

• Harmonized nameenv_monitoring_zone
• DescriptionAn environmental monitoring zone is a formal designation as part of an environmental monitoring program, in which areas of a food production facility are categorized, commonly as zones 1-4, based on likelihood or risk of foodborne pathogen contamination. This field accepts entries of zones 1-4, e.g., Zone 1

extreme weather event

• Harmonized nameextr_weather_event
• DescriptionUnusual weather events that may have affected microbial populations. Multiple terms can be separated by pipes, listed in reverse chronological order, e.g., hail

facility type

• Harmonized namefacility_type
• DescriptionEstablishment details about the type of facility where the sample was taken. This is independent of the specific product(s) within the facility, e.g., manufacturing-processing

farm equipment used

• Harmonized namefarm_equip
• DescriptionList of relevant equipment used for planting, fertilization, harvesting, irrigation, land levelling, residue management, weeding or transplanting during the growing season. This field encourages terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes, e.g., combine harvester [AGRO:00000473]

farm watering water source

• Harmonized namefarm_water_source
• DescriptionSource of water used on the farm for irrigation of crops or watering of livestock, e.g., water well

fertilizer administration

• Harmonized namefertilizer_admin
• DescriptionType of fertilizer or amendment added to the soil or water for the purpose of improving substrate health and quality for plant growth. This field encourages terms listed under agronomic fertilizer (http://purl.obolibrary.org/obo/AGRO_00002062). Multiple terms may apply and can be separated by pipes, listing in reverse chronological order, e.g., fish emulsion [AGRO:00000082]

food additive

• Harmonized namefood_additive
• DescriptionA 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 cleaning process

• Harmonized namefood_clean_proc
• DescriptionThe process of cleaning food to separate other environmental materials from the food source. Multiple terms can be separated by pipes, e.g., rinsed with water|scrubbed with brush

food contact surface

• Harmonized namefood_contact_surf
• DescriptionThe 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 namefood_contain_wrap
• DescriptionType 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]

FDA food industry class name

• Harmonized namefood_industry_class
• DescriptionThe US FDA Class is the second of five elements that comprise a FDA product code. This element is directly related to an Industry and designates the food group, source, product, use, pharmacological action, category or animal species of the product. A Class code is more specific than an Industry; for example, the Fishery/Seafood products Industry may contain Classes such as Smoked, Breaded and such, e.g., Coffee, Decaffeinated

FDA food industry code name

• Harmonized namefood_industry_code
• DescriptionThe US FDA Industry Code is the first of five elements that comprise an FDA product code. An Industry code determines the broadest area into which a product falls, e.g., 31 Coffee and Tea

food product origin geographic location

• Harmonized namefood_origin
• DescriptionA 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 packing integrity

• Harmonized namefood_pack_integrity
• DescriptionA 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 namefood_pack_medium
• DescriptionThe 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 namefood_preserv_proc
• DescriptionThe 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]

food processing method

• Harmonized namefood_processing_method
• DescriptionMethods for processing food, e.g., food (blanched) [FOODON:00002767]

food production system

• Harmonized namefood_prod
• DescriptionDescriptors of the food production system or of the agricultural environment and growing conditions related to the farm production system. This field encourages terms listed under food production (http://purl.obolibrary.org/obo/FOODON_03530206). Multiple terms may apply and can be separated by pipes, e.g., restaurant food preparation process [FOODON:03530110]

food product synonym

• Harmonized namefood_prod_synonym
• DescriptionOther names by which the food product is known by (e.g., regional or non-English names), e.g., pinot gris

food product type

• Harmonized namefood_product_type
• DescriptionA 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]

food quality date

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

food type processed in facility

• Harmonized namefood_type_processed
• DescriptionFood type processed in facility, e.g., dairy

host

• Harmonized namehost
• DescriptionThe natural (as opposed to laboratory) host to the organism from which the sample was obtained. Use the full taxonomic name, eg, "Homo sapiens".

host age

• Harmonized namehost_age
• DescriptionAge of host at the time of sampling

antimicrobial name

• Harmonized namehost_am
• DescriptionThe 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]

host animal breed

• Harmonized namehost_animal_breed
• DescriptionThe animal breed of the host organism. Used mainly for animal hosts, e.g., duroc, angus, mixed breed

host body product

• Harmonized namehost_body_product
• Descriptionsubstance produced by the host, e.g. stool, mucus, where the sample was obtained from

host disease

• Harmonized namehost_disease
• DescriptionName of relevant disease, e.g. Salmonella gastroenteritis. Controlled vocabulary, http://bioportal.bioontology.org/ontologies/1009 or http://www.ncbi.nlm.nih.gov/mesh

food animal group size

• Harmonized namehost_group_size
• DescriptionThe 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 namehost_housing
• DescriptionDescription 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]

host sex

• Harmonized namehost_sex
• DescriptionGender or physical sex of the host

host subject id

• Harmonized namehost_subject_id
• Descriptiona unique identifier by which each subject can be referred to, de-identified, e.g. #131

host tissue sampled

• Harmonized namehost_tissue_sampled
• Descriptionname of body site where the sample was obtained from, such as a specific organ or tissue, e.g., tongue, lung. For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON

host variety or cultivar

• Harmonized namehost_variety
• DescriptionThe variety or cultivar of the host organism; the name given to a particular variety of organism to distinguish it from otherwise similar organisms of the same species, e.g., romaine lettuce; Athena melons; Patio Snacker cucumbers

Interagency Food Safety Analytics Collaboration (IFSAC) category

• Harmonized nameifsac_category
• DescriptionThe 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

indoor surface

• Harmonized nameindoor_surf
• Descriptiontype of indoor surface

indoor sampling surface or structure subpart

• Harmonized nameindoor_surf_subpart
• DescriptionThe subpart of the object(s) that was swabbed, like a cart, drain, counter, etc., e.g., wheel

intended consumer

• Harmonized nameintended_consumer
• DescriptionFood consumer type, human or animal, for which the food product is produced and marketed, e.g., human

isolate name alias

• Harmonized nameisolate_name_alias
• DescriptionOther IDs associated with this isolate or strain. Separate with '; ' if more than one

labeling claims

• Harmonized namelabel_claims
• DescriptionDescriptors of the food production system such as wild caught, free-range, organic, free-range, industrial, hormone-free, antibiotic free, cage free, e.g., wild caught

latitude and longitude

• Harmonized namelat_lon
• DescriptionThe 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

location or room in facility

• Harmonized namelocation_in_facility
• DescriptionName of the location or room in the facility where the sampling occurred, e.g., ripening room

material condition

• Harmonized namematerial_condition
• DescriptionCondition of material sampled, e.g., rusted

mechanical damage

• Harmonized namemechanical_damage
• Descriptioninformation about any mechanical damage exerted on the plant; can include multiple damages and sites

plant growth medium

• Harmonized nameplant_growth_med
• DescriptionType of the media used for growing sampled plants, e.g., soil [ENVO:00001998]

plant water delivery method

• Harmonized nameplant_water_method
• DescriptionDescription of the equipment or method used to distribute water to crops. This field encourages terms listed under irrigation process (http://purl.obolibrary.org/obo/AGRO_00000006). Multiple terms can be separated by pipes, e.g., drip irrigation process [AGRO:00000056]

project name

• Harmonized nameproject_name
• DescriptionA concise name that describes the overall project, for example "Analysis of sequences collected from Antarctic soil"

reference material

• Harmonized namereference_material
• DescriptionIndicates that a standards body or external group asserts this sample is reference material, eg, 'NIST reference material for genome sequencing validation'.

relative location of sample

• Harmonized namerel_location
• DescriptionLocation of sample to other parts of the farm, e.g. under crop plant, near irrigation ditch, from the dirt road, from air above crops, nearby river, e.g., furrow

sample collection device or method

• Harmonized namesamp_collect_device
• DescriptionMethod or device employed for collecting sample

sanitizer used during postharvest cleaning

• Harmonized namesanitizer_used_postharvest
• DescriptionSubstance intended for preventing, neutralizing, destroying, repelling, or mitigating the effects of any pest or microorganism; indicate the sanitizer used during the postharvest cleaning process. Multiple terms can be separated by pipes, e.g., chlorine bleach

sequenced by

• Harmonized namesequenced_by
• DescriptionThe name of the agency that generated the sequence, e.g., Centers for Disease Control and Prevention

serotype

• Harmonized nameserotype
• DescriptionTaxonomy below subspecies; a variety (in bacteria, fungi or virus) usually based on its antigenic properties. Same as serovar and serogroup. e.g. serotype="H1N1" in Influenza A virus CY098518.

serovar

• Harmonized nameserovar
• DescriptionTaxonomy below subspecies; a variety (in bacteria, fungi or virus) usually based on its antigenic properties. Same as serovar and serotype. Sometimes used as species identifier in bacteria with shaky taxonomy, e.g. Leptospira, serovar saopaolo S76607 (65357 in Entrez).

soil type

• Harmonized namesoil_type
• Descriptionsoil series name or other lower-level classification

specific intended consumer

• Harmonized namespec_intended_cons
• DescriptionFood consumer type, human or animal, for which the food product is produced and marketed. This field encourages terms listed under food consumer group (http://purl.obolibrary.org/obo/FOODON_03510136), e.g., infant or toddler as food consumer [FOODON:03510020]

surface material

• Harmonized namesurf_material
• Descriptionsurface materials at the point of sampling

surface temperature

• Harmonized namesurf_temp
• Descriptiontemperature of the surface at the time of sampling

surface orientation

• Harmonized namesurface_orientation
• DescriptionDescribe which surface of the object is swabbed. (e.g underside, top, corner), e.g., underside

upstream intervention

• Harmonized nameupstream_intervention
• DescriptionList any known health-related interventions (prophylactic, therapeutic, and/or metaphylactic) administered to the host, i.e. vaccinations, hormonal patches, antibiotics, injections in feed, etc., e.g., prophylactic/metaphylactic antibiotics