Food-farm environment

Mandatory Attributes Optional Attributes

Mandatory Attributes

Biotic regimen

• Harmonized name: biotic_regm

• Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi

Chemical administration

• Harmonized name: chem_administration

• Description: list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v1.72), please see http://bioportal.bioontology.org/visualize/44603

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

Depth

• Harmonized name: depth

• Description: Depth is defined as the vertical distance below surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly. Depth can be reported as an interval for subsurface samples.

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 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

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

Sample material type (host or environmental context)

• Harmonized name: samp_mat_type

• Description: The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246)

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

Environment adjacent to site

• Harmonized name: adjacent_environment

• Description: Description: of the environmental system or features that are adjacent to the sampling site. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple terms can be separated by pipes

Local air flow impediments

• Harmonized name: air_flow_impede

• Description: Presence of objects in the area that would influence or impede air flow through the air filter, e.g., obstructed, unobstructed

Air particulate matter concentration

• Harmonized name: air_pm_concen

• Description: concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM

Ancestral data

• Harmonized name: ances_data

• Description: Information about either pedigree or other ancestral information Description: , e.g., parental variety in case of mutant or selection, A/3*B (meaning [(A x B) x B] x B)

Animal water delivery method

• Harmonized name: anim_water_method

• Description: Description: of the equipment or method used to distribute water to livestock. This field accepts terms listed under water delivery equipment (http://opendata.inra.fr/EOL/EOL_0001653). Multiple terms can be separated by pipes

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

Animal intrusion near sample source

• Harmonized name: animal_intrusion

• Description: Identification 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

Collection method

• Harmonized name: collection_method

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

Conductivity

• Harmonized name: conduc

• Description: electrical conductivity of water

Crop rotation

• Harmonized name: crop_rotation

• Description: whether or not crop is rotated, and if yes, rotation schedule

Crop yield

• Harmonized name: crop_yield

• Description: Amount of crop produced per unit or area of land

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

Extreme weather date

• Harmonized name: date_extr_weath

• Description: Date of unusual weather events that may have affected microbial populations. Multiple terms can be separated by pipes, listed in reverse chronological order

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

Extreme weather event

• Harmonized name: extr_weather_event

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

Farm equipment used

• Harmonized name: farm_equip

• Description: List 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 equipment sanitization

• Harmonized name: farm_equip_san

• Description: Method used to sanitize growing and harvesting equipment including type and concentration of sanitizing solution and frequency of sanitization

Farm equipment sanitization frequency

• Harmonized name: farm_equip_san_freq

• Description: The number of times farm equipment is cleaned. Frequency of cleaning might be on a daily basis, weekly, monthly, quarterly or annually

Equipment shared with other farms

• Harmonized name: farm_equip_shared

• Description: List of planting, growing or harvesting equipment shared with other farms

Farm watering water source

• Harmonized name: farm_water_source

• Description: Source of water used on the farm for irrigation of crops or watering of livestock, e.g., water well

Fertilizer administration

• Harmonized name: fertilizer_admin

• Description: Type 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]

Fertilizer administration date

• Harmonized name: fertilizer_date

• Description: Date of administration of soil amendment or fertilizer. Multiple terms may apply and can be separated by pipes, listing in reverse chronological order

Food cleaning process

• Harmonized name: food_clean_proc

• Description: The 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 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 harvesting process

• Harmonized name: food_harvest_proc

• Description: A harvesting process is a process which takes in some food material from an individual or community of plant or animal organisms in a given context and time, and outputs a precursor or consumable food product. This may include a part of an organism or the whole, and may involve killing the organism

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]

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 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 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)

Genetic modification

• Harmonized name: genetic_mod

• Description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection

Growth habit

• Harmonized name: growth_habit

• Description: Characteristic shape, appearance or growth form of a plant species, e.g., erect, semi-erect, spreading, prostrate

Growth medium

• Harmonized name: growth_medium

• 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). The name of the medium used to grow the microorganism

Host age

• Harmonized name: host_age

• Description: Age of host at the time of sampling

Host disease

• Harmonized name: host_disease

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

Host dry mass

• Harmonized name: host_dry_mass

• Description: measurement of dry mass

Host genotype

• Harmonized name: host_genotype

• Description:

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

Host height

• Harmonized name: host_height

• Description: the height of subject

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]

Host length

• Harmonized name: host_length

• Description: the length of subject

Host phenotype

• Harmonized name: host_phenotype

Host subspecific genetic lineage

• Harmonized name: host_subspecf_genlin

• Description: Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123

Host taxonomy ID

• Harmonized name: host_taxid

• Description: NCBI taxonomy ID of the host, e.g. 9606

Host total mass

• Harmonized name: host_tot_mass

• Description: total mass of the host at collection, the unit depends on host

Humidity

• Harmonized name: humidity

• Description: amount of water vapour in the air, at the time of sampling

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

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

Mechanical damage

• Harmonized name: mechanical_damage

• Description: information about any mechanical damage exerted on the plant; can include multiple damages and sites

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

pH

• Harmonized name: ph

• Description: pH measurement

pH method

• Harmonized name: ph_meth

• Description: reference or method used in determining pH

Plant growth medium

• Harmonized name: plant_growth_med

• Description: Type of the media used for growing sampled plants, e.g., soil [ENVO:00001998]

Degree of plant part maturity

• Harmonized name: plant_part_maturity

• Description: A Description: of the stage of development of a plant or plant part based on maturity or ripeness. This field accepts terms listed under degree of plant maturity (http://purl.obolibrary.org/obo/FOODON_03530050)

Plant reproductive part

• Harmonized name: plant_reprod_crop

• Description: Plant reproductive part used in the field during planting to start the crop, e.g., plant cutting, pregerminated seed, ratoon, seed, seedling, whole mature plant

Plant water delivery method

• Harmonized name: plant_water_method

• Description: Description: 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]

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

Previous land use

• Harmonized name: previous_land_use

• Description: previous land use and dates

Production labeling claims

• Harmonized name: prod_label_claims

• Description: Labeling claims containing descriptors such as wild caught, free-range, organic, free-range, industrial, hormone-free, antibiotic free, cage free

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

Reference for biomaterial

• Harmonized name: ref_biomaterial

• Description: Primary publication or genome report

Relative location of sample

• Harmonized name: rel_location

• Description: Location 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

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

Rooting conditions

• Harmonized name: root_cond

• Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container

Rooting medium carbon

• Harmonized name: root_med_carbon

• Description: Source of organic carbon in the culture rooting medium, e.g., sucrose

Rooting medium macronutrients

• Harmonized name: root_med_macronutr

• Description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S), e.g., KH2PO4 (170mg/L)

Rooting medium micronutrients

• Harmonized name: root_med_micronutr

• Description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo), e.g., H3BO3 (6.2mg/L)

Rooting medium pH

• Harmonized name: root_med_ph

• Description: pH measurement of the culture rooting medium, e.g., 5.5

Salinity

• Harmonized name: salinity

• Description: salinity measurement

Salinity method

• Harmonized name: salinity_meth

• Description: reference or method used in determining salinity

Sample collection device or method

• Harmonized name: samp_collect_device

• Description: Method or device employed for collecting 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

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 duration

• Harmonized name: samp_store_dur

Sample storage temperature

• Harmonized name: samp_store_temp

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

Season

• Harmonized name: season

• Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729)

Mean seasonal humidity

• Harmonized name: season_humidity

• Description: Average humidity of the region throughout the growing season

Mean seasonal precipitation

• Harmonized name: season_precpt

• Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps

Mean seasonal temperature

• Harmonized name: season_temp

• Description: Mean seasonal temperature

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

Size-fraction lower threshold

• Harmonized name: size_frac_low

• Description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample

Size-fraction upper threshold

• Harmonized name: size_frac_up

• Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample

Soil conductivity

• Harmonized name: soil_conductivity

• Description: Conductivity of soil at time of sampling

Soil cover

• Harmonized name: soil_cover

• Description: Description: of the material covering the sampled soil. This field accepts terms under ENVO:00010483, environmental material

Soil pH

• Harmonized name: soil_ph

• Description: The pH of soil at time of sampling

Soil sediment porosity

• Harmonized name: soil_porosity

• Description: Porosity of soil or deposited sediment is volume of voids divided by the total volume of sample

Soil temperature

• Harmonized name: soil_temp

• Description: Temperature of soil at the time of sampling

Soil texture classification

• Harmonized name: soil_texture_class

• Description: One of the 12 soil texture classes use to describe soil texture based on the relative proportion of different grain sizes of mineral particles [sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um)] in a soil, e.g., clay, clay loam, loam, loamy sand, sand, sandy clay, sandy clay loam, sandy loam, silt, silty clay, silty clay loam, silt loam

Soil texture method

• Harmonized name: soil_texture_meth

• Description: reference or method used in determining soil texture

Soil type

• Harmonized name: soil_type

• Description: soil series name or other lower-level classification

Soil type method

• Harmonized name: soil_type_meth

• Description: reference or method used in determining soil series name or other lower-level classification

Solar irradiance

• Harmonized name: solar_irradiance

• Description: the amount of solar energy that arrives at a specific area of a surface during a specific time interval

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.

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

Temperature

• Harmonized name: temp

• Description: temperature of the sample at time of sampling

Tillage

• Harmonized name: tillage

• Description: note method(s) used for tilling

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

Total nitrogen

• Harmonized name: tot_nitro

• Description: total nitrogen content of the sample

Total nitrogen content method

• Harmonized name: tot_nitro_cont_meth

• Description: Reference or method used in determining the total nitrogen

Total organic carbon method

• Harmonized name: tot_org_c_meth

• Description: reference or method used in determining total organic C

Total organic carbon

• Harmonized name: tot_org_carb

• Description: Definition for soil: total organic C content of the soil units of g C/kg soil. Definition otherwise: total organic carbon content

Turbidity

• Harmonized name: turbidity

• Description: turbidity measurement

Ventilation rate

• Harmonized name: ventilation_rate

• Description: ventilation rate of the system in the sampled premises

Ventilation type

• Harmonized name: ventilation_type

• Description: ventilation system used in the sampled premises

Water delivery frequency

• Harmonized name: water_frequency

• Description: Number of water delivery events within a given period of time

Water pH

• Harmonized name: water_ph

• Description: The pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid

Environmental feature adjacent water source

• Harmonized name: water_source_adjac

• Description: Description: of the environmental features that are adjacent to the farm water source. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple terms can be separated by pipes

Water source shared

• Harmonized name: water_source_shared

• Description: Other users sharing access to the same water source, e.g., multiple users, agricutural, multiple users, no sharing

Wind direction

• Harmonized name: wind_direction

• Description: wind direction is the direction from which a wind originates

Wind speed

• Harmonized name: wind_speed

• Description: speed of wind measured at the time of sampling