Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant
gram, mole per liter, milligram per liter, microgram per cubic meter
Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound
volatile organic compound name;measurement value
microgram per cubic meter, parts per million, nanogram per liter
Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values
Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor
Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present
travel outside the country in last six months
Specification of the countries travelled in the last six months; can include multiple travels
History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850)
Report any history of nose, mouth, teeth and/or throat disorders in the subject. May include multiple disorders.
The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974)
History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74)
History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557)
History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18)
History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77)
History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409)
History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974)
History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37)
History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229)
History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18)
Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens
temperature value;treatment interval and duration
Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens
antibiotic name;antibiotic amount;treatment interval and duration
Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens
mutagen name;mutagen amount;treatment interval and duration
Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens
fertilizer name;fertilizer amount;treatment interval and duration
gram, mole per liter, milligram per liter
Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments
gravity factor value;treatment interval and duration
Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens
growth hormone name;growth hormone amount;treatment interval and duration
Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
humidity value;treatment interval and duration
Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens
mineral nutrient name;mineral nutrient amount;treatment interval and duration
Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens
radiation type name;radiation amount;treatment interval and duration
Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
measurement value;treatment interval and duration
Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field
Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types
Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances
gaseous substance name;measurement value
Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles
inorganic particle name;measurement value
Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc
Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc
soluble inorganic material name;measurement value
gram, microgram, mole per liter, gram per liter, parts per million
Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc
soluble organic material name;measurement value
The primary function for which a building or discrete part of a building is intended to be used
A device which removes solid particulates or airborne molecular contaminants
Methods of conditioning or heating a room or building
The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level
Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light
Any drug used by subject and the frequency of usage; can include multiple drugs used
Specification of special diet; can include multiple special diets
Measurement of atmospheric data; can include multiple data
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 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
environmental feature adjacent water source
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
Unusual weather events that may have affected microbial populations. Multiple terms can be separated by pipes, listed in reverse chronological order
Date of unusual weather events that may have affected microbial populations. Multiple terms can be separated by pipes, listed in reverse chronological order
Presence of objects in the area that would influence or impede air flow through the air filter
enumeration;obstruction type; distance from sampling device
Plant reproductive part used in the field during planting to start the crop
Any chemicals that are added to the fermentation process to achieve the desired final product
fermentation chemical additives percentage
The amount of chemical added to the fermentation process
Food consumer type, human or animal, for which the food product is produced and marketed. This field accepts terms listed under food consumer group (http://purl.obolibrary.org/obo/FOODON_03510136)
Establishment details about the type of facility where the sample was taken. This is independent of the specific product(s) within the facility
Degree of water held on a sampled surface. If present, user can state the degree of water held on surface (intermittent moisture, submerged). If no surface moisture is present indicate not present
Substance intended for preventing, neutralizing, destroying, repelling, or mitigating the effects of any pest or microorganism; that inhibits the growth, reproduction, and activity of organisms, including fungal cells; decreases the number of fungi or pests present; deters microbial growth and degradation of other ingredients in the formulation. Indicate the biocide used on the location where the sample was taken. Multiple terms can be separated by pipes
commercial name of biocide, active ingredient in biocide or class of biocide
The method used to sterilize the sampling room. This field accepts terms listed under electromagnetic radiation (http://purl.obolibrary.org/obo/ENVO_01001026). If the proper descriptor is not listed, please use text to describe the sampling room sterilization method. Multiple terms can be separated by pipes
host of the symbiotic host disease status
List of diseases with which the host of the symbiotic host organism has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text
host of the symbiotic host local environmental context
For a symbiotic host organism the local anatomical environment within its host may have causal influences. Report the anatomical entity(s) which are in the direct environment of the symbiotic host organism being sampled and which you believe have significant causal influences on your sample or specimen. For example, if the symbiotic host organism being sampled is an intestinal worm, its local environmental context will be the term for intestine from UBERON (http://uberon.github.io/)
UBERON term(s), multiple values can be separated by pipes
host of the symbiotic host family relationship
Familial relationship of the host of the symbiotic host organisms to other hosts of symbiotic host organism in the same study; can include multiple relationships
Reference or method used in measurement of photosythetic activity
The element and mass number of the stable isotope used in isotopologue labeling.
Isotopologue (isotope source/substrate/molecule) added to the biological sample.
List the PubChem Compound Identification (CID) number. If it's an undefined mixture, enter 0.
MIxS Data that comply with the MigsEu checklist and the Air Extension
MIxS Data that comply with the MigsEu checklist and the BuiltEnvironment Extension
MIxS Data that comply with the MigsEu checklist and the HostAssociated Extension
MIxS Data that comply with the MigsEu checklist and the HumanAssociated Extension
MIxS Data that comply with the MigsEu checklist and the HumanGut Extension
MIxS Data that comply with the MigsEu checklist and the HumanOral Extension
MIxS Data that comply with the MigsEu checklist and the HumanSkin Extension
MIxS Data that comply with the MigsEu checklist and the HumanVaginal Extension
MigsEu combined with MicrobialMatBiofilm
MIxS Data that comply with the MigsEu checklist and the MicrobialMatBiofilm Extension
MigsEu combined with MiscellaneousNaturalOrArtificialEnvironment
MIxS Data that comply with the MigsEu checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension
MIxS Data that comply with the MigsEu checklist and the PlantAssociated Extension
MIxS Data that comply with the MigsEu checklist and the Sediment Extension
MIxS Data that comply with the MigsEu checklist and the Soil Extension
MIxS Data that comply with the MigsEu checklist and the WastewaterSludge Extension
MIxS Data that comply with the MigsEu checklist and the Water Extension
MigsEu combined with HydrocarbonResourcesCores
MIxS Data that comply with the MigsEu checklist and the HydrocarbonResourcesCores Extension
MigsEu combined with HydrocarbonResourcesFluidsSwabs
MIxS Data that comply with the MigsEu checklist and the HydrocarbonResourcesFluidsSwabs Extension
MIxS Data that comply with the MigsEu checklist and the Agriculture Extension
MigsEu combined with FoodAnimalAndAnimalFeed
MIxS Data that comply with the MigsEu checklist and the FoodAnimalAndAnimalFeed Extension
MigsEu combined with FoodFarmEnvironment
MIxS Data that comply with the MigsEu checklist and the FoodFarmEnvironment Extension
MigsEu combined with FoodFoodProductionFacility
MIxS Data that comply with the MigsEu checklist and the FoodFoodProductionFacility Extension
MIxS Data that comply with the MigsEu checklist and the FoodHumanFoods Extension
MIxS Data that comply with the MigsEu checklist and the SymbiontAssociated Extension
MIxS Data that comply with the MigsBa checklist and the Air Extension
MIxS Data that comply with the MigsBa checklist and the BuiltEnvironment Extension
MIxS Data that comply with the MigsBa checklist and the HostAssociated Extension
MIxS Data that comply with the MigsBa checklist and the HumanAssociated Extension
MIxS Data that comply with the MigsBa checklist and the HumanGut Extension
MIxS Data that comply with the MigsBa checklist and the HumanOral Extension
MIxS Data that comply with the MigsBa checklist and the HumanSkin Extension
MIxS Data that comply with the MigsBa checklist and the HumanVaginal Extension
MigsBa combined with MicrobialMatBiofilm
MIxS Data that comply with the MigsBa checklist and the MicrobialMatBiofilm Extension
MigsBa combined with MiscellaneousNaturalOrArtificialEnvironment
MIxS Data that comply with the MigsBa checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension
MIxS Data that comply with the MigsBa checklist and the PlantAssociated Extension
MIxS Data that comply with the MigsBa checklist and the Sediment Extension
MIxS Data that comply with the MigsBa checklist and the Soil Extension
MIxS Data that comply with the MigsBa checklist and the WastewaterSludge Extension
MIxS Data that comply with the MigsBa checklist and the Water Extension
MigsBa combined with HydrocarbonResourcesCores
MIxS Data that comply with the MigsBa checklist and the HydrocarbonResourcesCores Extension
MigsBa combined with HydrocarbonResourcesFluidsSwabs
MIxS Data that comply with the MigsBa checklist and the HydrocarbonResourcesFluidsSwabs Extension
MIxS Data that comply with the MigsBa checklist and the Agriculture Extension
MigsBa combined with FoodAnimalAndAnimalFeed
MIxS Data that comply with the MigsBa checklist and the FoodAnimalAndAnimalFeed Extension
MigsBa combined with FoodFarmEnvironment
MIxS Data that comply with the MigsBa checklist and the FoodFarmEnvironment Extension
MigsBa combined with FoodFoodProductionFacility
MIxS Data that comply with the MigsBa checklist and the FoodFoodProductionFacility Extension
MIxS Data that comply with the MigsBa checklist and the FoodHumanFoods Extension
MIxS Data that comply with the MigsBa checklist and the SymbiontAssociated Extension
MIxS Data that comply with the MigsPl checklist and the Air Extension
MIxS Data that comply with the MigsPl checklist and the BuiltEnvironment Extension
MIxS Data that comply with the MigsPl checklist and the HostAssociated Extension
MIxS Data that comply with the MigsPl checklist and the HumanAssociated Extension
MIxS Data that comply with the MigsPl checklist and the HumanGut Extension
MIxS Data that comply with the MigsPl checklist and the HumanOral Extension
MIxS Data that comply with the MigsPl checklist and the HumanSkin Extension
MIxS Data that comply with the MigsPl checklist and the HumanVaginal Extension
MigsPl combined with MicrobialMatBiofilm
MIxS Data that comply with the MigsPl checklist and the MicrobialMatBiofilm Extension
MigsPl combined with MiscellaneousNaturalOrArtificialEnvironment
MIxS Data that comply with the MigsPl checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension
MIxS Data that comply with the MigsPl checklist and the PlantAssociated Extension
MIxS Data that comply with the MigsPl checklist and the Sediment Extension
MIxS Data that comply with the MigsPl checklist and the Soil Extension
MIxS Data that comply with the MigsPl checklist and the WastewaterSludge Extension
MIxS Data that comply with the MigsPl checklist and the Water Extension
MigsPl combined with HydrocarbonResourcesCores
MIxS Data that comply with the MigsPl checklist and the HydrocarbonResourcesCores Extension
MigsPl combined with HydrocarbonResourcesFluidsSwabs
MIxS Data that comply with the MigsPl checklist and the HydrocarbonResourcesFluidsSwabs Extension
MIxS Data that comply with the MigsPl checklist and the Agriculture Extension
MigsPl combined with FoodAnimalAndAnimalFeed
MIxS Data that comply with the MigsPl checklist and the FoodAnimalAndAnimalFeed Extension
MigsPl combined with FoodFarmEnvironment
MIxS Data that comply with the MigsPl checklist and the FoodFarmEnvironment Extension
MigsPl combined with FoodFoodProductionFacility
MIxS Data that comply with the MigsPl checklist and the FoodFoodProductionFacility Extension
MIxS Data that comply with the MigsPl checklist and the FoodHumanFoods Extension
MIxS Data that comply with the MigsPl checklist and the SymbiontAssociated Extension
MIxS Data that comply with the MigsVi checklist and the Air Extension
MIxS Data that comply with the MigsVi checklist and the BuiltEnvironment Extension
MIxS Data that comply with the MigsVi checklist and the HostAssociated Extension
MIxS Data that comply with the MigsVi checklist and the HumanAssociated Extension
MIxS Data that comply with the MigsVi checklist and the HumanGut Extension
MIxS Data that comply with the MigsVi checklist and the HumanOral Extension
MIxS Data that comply with the MigsVi checklist and the HumanSkin Extension
MIxS Data that comply with the MigsVi checklist and the HumanVaginal Extension
MigsVi combined with MicrobialMatBiofilm
MIxS Data that comply with the MigsVi checklist and the MicrobialMatBiofilm Extension
MigsVi combined with MiscellaneousNaturalOrArtificialEnvironment
MIxS Data that comply with the MigsVi checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension
MIxS Data that comply with the MigsVi checklist and the PlantAssociated Extension
MIxS Data that comply with the MigsVi checklist and the Sediment Extension
MIxS Data that comply with the MigsVi checklist and the Soil Extension
MIxS Data that comply with the MigsVi checklist and the WastewaterSludge Extension
MIxS Data that comply with the MigsVi checklist and the Water Extension
MigsVi combined with HydrocarbonResourcesCores
MIxS Data that comply with the MigsVi checklist and the HydrocarbonResourcesCores Extension
MigsVi combined with HydrocarbonResourcesFluidsSwabs
MIxS Data that comply with the MigsVi checklist and the HydrocarbonResourcesFluidsSwabs Extension
MIxS Data that comply with the MigsVi checklist and the Agriculture Extension
MigsVi combined with FoodAnimalAndAnimalFeed
MIxS Data that comply with the MigsVi checklist and the FoodAnimalAndAnimalFeed Extension
MigsVi combined with FoodFarmEnvironment
MIxS Data that comply with the MigsVi checklist and the FoodFarmEnvironment Extension
MigsVi combined with FoodFoodProductionFacility
MIxS Data that comply with the MigsVi checklist and the FoodFoodProductionFacility Extension
MIxS Data that comply with the MigsVi checklist and the FoodHumanFoods Extension
MIxS Data that comply with the MigsVi checklist and the SymbiontAssociated Extension
MIxS Data that comply with the MigsOrg checklist and the Air Extension
MIxS Data that comply with the MigsOrg checklist and the BuiltEnvironment Extension
MIxS Data that comply with the MigsOrg checklist and the HostAssociated Extension
MIxS Data that comply with the MigsOrg checklist and the HumanAssociated Extension
MIxS Data that comply with the MigsOrg checklist and the HumanGut Extension
MIxS Data that comply with the MigsOrg checklist and the HumanOral Extension
MIxS Data that comply with the MigsOrg checklist and the HumanSkin Extension
MIxS Data that comply with the MigsOrg checklist and the HumanVaginal Extension
MigsOrg combined with MicrobialMatBiofilm
MIxS Data that comply with the MigsOrg checklist and the MicrobialMatBiofilm Extension
MigsOrg combined with MiscellaneousNaturalOrArtificialEnvironment
MIxS Data that comply with the MigsOrg checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension
MIxS Data that comply with the MigsOrg checklist and the PlantAssociated Extension
MIxS Data that comply with the MigsOrg checklist and the Sediment Extension
MIxS Data that comply with the MigsOrg checklist and the Soil Extension
MIxS Data that comply with the MigsOrg checklist and the WastewaterSludge Extension
MIxS Data that comply with the MigsOrg checklist and the Water Extension
MigsOrg combined with HydrocarbonResourcesCores
MIxS Data that comply with the MigsOrg checklist and the HydrocarbonResourcesCores Extension
MigsOrg combined with HydrocarbonResourcesFluidsSwabs
MIxS Data that comply with the MigsOrg checklist and the HydrocarbonResourcesFluidsSwabs Extension
MIxS Data that comply with the MigsOrg checklist and the Agriculture Extension
MigsOrg combined with FoodAnimalAndAnimalFeed
MIxS Data that comply with the MigsOrg checklist and the FoodAnimalAndAnimalFeed Extension
MigsOrg combined with FoodFarmEnvironment
MIxS Data that comply with the MigsOrg checklist and the FoodFarmEnvironment Extension
MigsOrg combined with FoodFoodProductionFacility
MIxS Data that comply with the MigsOrg checklist and the FoodFoodProductionFacility Extension
MIxS Data that comply with the MigsOrg checklist and the FoodHumanFoods Extension
MigsOrg combined with SymbiontAssociated
MIxS Data that comply with the MigsOrg checklist and the SymbiontAssociated Extension
MIxS Data that comply with the Mims checklist and the Air Extension
MIxS Data that comply with the Mims checklist and the BuiltEnvironment Extension
MIxS Data that comply with the Mims checklist and the HostAssociated Extension
MIxS Data that comply with the Mims checklist and the HumanAssociated Extension
MIxS Data that comply with the Mims checklist and the HumanGut Extension
MIxS Data that comply with the Mims checklist and the HumanOral Extension
MIxS Data that comply with the Mims checklist and the HumanSkin Extension
MIxS Data that comply with the Mims checklist and the HumanVaginal Extension
MIxS Data that comply with the Mims checklist and the MicrobialMatBiofilm Extension
Mims combined with MiscellaneousNaturalOrArtificialEnvironment
MIxS Data that comply with the Mims checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension
MIxS Data that comply with the Mims checklist and the PlantAssociated Extension
MIxS Data that comply with the Mims checklist and the Sediment Extension
MIxS Data that comply with the Mims checklist and the Soil Extension
MIxS Data that comply with the Mims checklist and the WastewaterSludge Extension
MIxS Data that comply with the Mims checklist and the Water Extension
Mims combined with HydrocarbonResourcesCores
MIxS Data that comply with the Mims checklist and the HydrocarbonResourcesCores Extension
Mims combined with HydrocarbonResourcesFluidsSwabs
MIxS Data that comply with the Mims checklist and the HydrocarbonResourcesFluidsSwabs Extension
MIxS Data that comply with the Mims checklist and the Agriculture Extension
Mims combined with FoodAnimalAndAnimalFeed
MIxS Data that comply with the Mims checklist and the FoodAnimalAndAnimalFeed Extension
MIxS Data that comply with the Mims checklist and the FoodFarmEnvironment Extension
Mims combined with FoodFoodProductionFacility
MIxS Data that comply with the Mims checklist and the FoodFoodProductionFacility Extension
MIxS Data that comply with the Mims checklist and the FoodHumanFoods Extension
MIxS Data that comply with the Mims checklist and the SymbiontAssociated Extension
MIxS Data that comply with the MimarksS checklist and the Air Extension
MIxS Data that comply with the MimarksS checklist and the BuiltEnvironment Extension
MIxS Data that comply with the MimarksS checklist and the HostAssociated Extension
MIxS Data that comply with the MimarksS checklist and the HumanAssociated Extension
MIxS Data that comply with the MimarksS checklist and the HumanGut Extension
MIxS Data that comply with the MimarksS checklist and the HumanOral Extension
MIxS Data that comply with the MimarksS checklist and the HumanSkin Extension
MIxS Data that comply with the MimarksS checklist and the HumanVaginal Extension
MimarksS combined with MicrobialMatBiofilm
MIxS Data that comply with the MimarksS checklist and the MicrobialMatBiofilm Extension
MimarksS combined with MiscellaneousNaturalOrArtificialEnvironment
MIxS Data that comply with the MimarksS checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension
MIxS Data that comply with the MimarksS checklist and the PlantAssociated Extension
MIxS Data that comply with the MimarksS checklist and the Sediment Extension
MIxS Data that comply with the MimarksS checklist and the Soil Extension
MIxS Data that comply with the MimarksS checklist and the WastewaterSludge Extension
MIxS Data that comply with the MimarksS checklist and the Water Extension
MimarksS combined with HydrocarbonResourcesCores
MIxS Data that comply with the MimarksS checklist and the HydrocarbonResourcesCores Extension
MimarksS combined with HydrocarbonResourcesFluidsSwabs
MIxS Data that comply with the MimarksS checklist and the HydrocarbonResourcesFluidsSwabs Extension
MIxS Data that comply with the MimarksS checklist and the Agriculture Extension
MimarksS combined with FoodAnimalAndAnimalFeed
MIxS Data that comply with the MimarksS checklist and the FoodAnimalAndAnimalFeed Extension
MimarksS combined with FoodFarmEnvironment
MIxS Data that comply with the MimarksS checklist and the FoodFarmEnvironment Extension
MimarksS combined with FoodFoodProductionFacility
MIxS Data that comply with the MimarksS checklist and the FoodFoodProductionFacility Extension
MIxS Data that comply with the MimarksS checklist and the FoodHumanFoods Extension
MimarksS combined with SymbiontAssociated
MIxS Data that comply with the MimarksS checklist and the SymbiontAssociated Extension
MIxS Data that comply with the MimarksC checklist and the Air Extension
MIxS Data that comply with the MimarksC checklist and the BuiltEnvironment Extension
MIxS Data that comply with the MimarksC checklist and the HostAssociated Extension
MIxS Data that comply with the MimarksC checklist and the HumanAssociated Extension
MIxS Data that comply with the MimarksC checklist and the HumanGut Extension
MIxS Data that comply with the MimarksC checklist and the HumanOral Extension
MIxS Data that comply with the MimarksC checklist and the HumanSkin Extension
MIxS Data that comply with the MimarksC checklist and the HumanVaginal Extension
MimarksC combined with MicrobialMatBiofilm
MIxS Data that comply with the MimarksC checklist and the MicrobialMatBiofilm Extension
MimarksC combined with MiscellaneousNaturalOrArtificialEnvironment
MIxS Data that comply with the MimarksC checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension
MIxS Data that comply with the MimarksC checklist and the PlantAssociated Extension
MIxS Data that comply with the MimarksC checklist and the Sediment Extension
MIxS Data that comply with the MimarksC checklist and the Soil Extension
MIxS Data that comply with the MimarksC checklist and the WastewaterSludge Extension
MIxS Data that comply with the MimarksC checklist and the Water Extension
MimarksC combined with HydrocarbonResourcesCores
MIxS Data that comply with the MimarksC checklist and the HydrocarbonResourcesCores Extension
MimarksC combined with HydrocarbonResourcesFluidsSwabs
MIxS Data that comply with the MimarksC checklist and the HydrocarbonResourcesFluidsSwabs Extension
MIxS Data that comply with the MimarksC checklist and the Agriculture Extension
MimarksC combined with FoodAnimalAndAnimalFeed
MIxS Data that comply with the MimarksC checklist and the FoodAnimalAndAnimalFeed Extension
MimarksC combined with FoodFarmEnvironment
MIxS Data that comply with the MimarksC checklist and the FoodFarmEnvironment Extension
MimarksC combined with FoodFoodProductionFacility
MIxS Data that comply with the MimarksC checklist and the FoodFoodProductionFacility Extension
MIxS Data that comply with the MimarksC checklist and the FoodHumanFoods Extension
MimarksC combined with SymbiontAssociated
MIxS Data that comply with the MimarksC checklist and the SymbiontAssociated Extension
MIxS Data that comply with the Misag checklist and the Air Extension
MIxS Data that comply with the Misag checklist and the BuiltEnvironment Extension
MIxS Data that comply with the Misag checklist and the HostAssociated Extension
MIxS Data that comply with the Misag checklist and the HumanAssociated Extension
MIxS Data that comply with the Misag checklist and the HumanGut Extension
MIxS Data that comply with the Misag checklist and the HumanOral Extension
MIxS Data that comply with the Misag checklist and the HumanSkin Extension
MIxS Data that comply with the Misag checklist and the HumanVaginal Extension
MIxS Data that comply with the Misag checklist and the MicrobialMatBiofilm Extension
Misag combined with MiscellaneousNaturalOrArtificialEnvironment
MIxS Data that comply with the Misag checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension
MIxS Data that comply with the Misag checklist and the PlantAssociated Extension
MIxS Data that comply with the Misag checklist and the Sediment Extension
MIxS Data that comply with the Misag checklist and the Soil Extension
MIxS Data that comply with the Misag checklist and the WastewaterSludge Extension
MIxS Data that comply with the Misag checklist and the Water Extension
Misag combined with HydrocarbonResourcesCores
MIxS Data that comply with the Misag checklist and the HydrocarbonResourcesCores Extension
Misag combined with HydrocarbonResourcesFluidsSwabs
MIxS Data that comply with the Misag checklist and the HydrocarbonResourcesFluidsSwabs Extension
MIxS Data that comply with the Misag checklist and the Agriculture Extension
Misag combined with FoodAnimalAndAnimalFeed
MIxS Data that comply with the Misag checklist and the FoodAnimalAndAnimalFeed Extension
MIxS Data that comply with the Misag checklist and the FoodFarmEnvironment Extension
Misag combined with FoodFoodProductionFacility
MIxS Data that comply with the Misag checklist and the FoodFoodProductionFacility Extension
MIxS Data that comply with the Misag checklist and the FoodHumanFoods Extension
MIxS Data that comply with the Misag checklist and the SymbiontAssociated Extension
MIxS Data that comply with the Mimag checklist and the Air Extension
MIxS Data that comply with the Mimag checklist and the BuiltEnvironment Extension
MIxS Data that comply with the Mimag checklist and the HostAssociated Extension
MIxS Data that comply with the Mimag checklist and the HumanAssociated Extension
MIxS Data that comply with the Mimag checklist and the HumanGut Extension
MIxS Data that comply with the Mimag checklist and the HumanOral Extension
MIxS Data that comply with the Mimag checklist and the HumanSkin Extension
MIxS Data that comply with the Mimag checklist and the HumanVaginal Extension
MIxS Data that comply with the Mimag checklist and the MicrobialMatBiofilm Extension
Mimag combined with MiscellaneousNaturalOrArtificialEnvironment
MIxS Data that comply with the Mimag checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension
MIxS Data that comply with the Mimag checklist and the PlantAssociated Extension
MIxS Data that comply with the Mimag checklist and the Sediment Extension
MIxS Data that comply with the Mimag checklist and the Soil Extension
MIxS Data that comply with the Mimag checklist and the WastewaterSludge Extension
MIxS Data that comply with the Mimag checklist and the Water Extension
Mimag combined with HydrocarbonResourcesCores
MIxS Data that comply with the Mimag checklist and the HydrocarbonResourcesCores Extension
Mimag combined with HydrocarbonResourcesFluidsSwabs
MIxS Data that comply with the Mimag checklist and the HydrocarbonResourcesFluidsSwabs Extension
MIxS Data that comply with the Mimag checklist and the Agriculture Extension
Mimag combined with FoodAnimalAndAnimalFeed
MIxS Data that comply with the Mimag checklist and the FoodAnimalAndAnimalFeed Extension
MIxS Data that comply with the Mimag checklist and the FoodFarmEnvironment Extension
Mimag combined with FoodFoodProductionFacility
MIxS Data that comply with the Mimag checklist and the FoodFoodProductionFacility Extension
MIxS Data that comply with the Mimag checklist and the FoodHumanFoods Extension
MIxS Data that comply with the Mimag checklist and the SymbiontAssociated Extension
MIxS Data that comply with the Miuvig checklist and the Air Extension
MIxS Data that comply with the Miuvig checklist and the BuiltEnvironment Extension
MIxS Data that comply with the Miuvig checklist and the HostAssociated Extension
MIxS Data that comply with the Miuvig checklist and the HumanAssociated Extension
MIxS Data that comply with the Miuvig checklist and the HumanGut Extension
MIxS Data that comply with the Miuvig checklist and the HumanOral Extension
MIxS Data that comply with the Miuvig checklist and the HumanSkin Extension
MIxS Data that comply with the Miuvig checklist and the HumanVaginal Extension
Miuvig combined with MicrobialMatBiofilm
MIxS Data that comply with the Miuvig checklist and the MicrobialMatBiofilm Extension
Miuvig combined with MiscellaneousNaturalOrArtificialEnvironment
MIxS Data that comply with the Miuvig checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension
MIxS Data that comply with the Miuvig checklist and the PlantAssociated Extension
MIxS Data that comply with the Miuvig checklist and the Sediment Extension
MIxS Data that comply with the Miuvig checklist and the Soil Extension
MIxS Data that comply with the Miuvig checklist and the WastewaterSludge Extension
MIxS Data that comply with the Miuvig checklist and the Water Extension
Miuvig combined with HydrocarbonResourcesCores
MIxS Data that comply with the Miuvig checklist and the HydrocarbonResourcesCores Extension
Miuvig combined with HydrocarbonResourcesFluidsSwabs
MIxS Data that comply with the Miuvig checklist and the HydrocarbonResourcesFluidsSwabs Extension
MIxS Data that comply with the Miuvig checklist and the Agriculture Extension
Miuvig combined with FoodAnimalAndAnimalFeed
MIxS Data that comply with the Miuvig checklist and the FoodAnimalAndAnimalFeed Extension
Miuvig combined with FoodFarmEnvironment
MIxS Data that comply with the Miuvig checklist and the FoodFarmEnvironment Extension
Miuvig combined with FoodFoodProductionFacility
MIxS Data that comply with the Miuvig checklist and the FoodFoodProductionFacility Extension
MIxS Data that comply with the Miuvig checklist and the FoodHumanFoods Extension
MIxS Data that comply with the Miuvig checklist and the SymbiontAssociated Extension
MIxS Data that comply with the MimsMisip checklist and the Air Extension
MimsMisip combined with BuiltEnvironment
MIxS Data that comply with the MimsMisip checklist and the BuiltEnvironment Extension
MIxS Data that comply with the MimsMisip checklist and the HostAssociated Extension
MIxS Data that comply with the MimsMisip checklist and the HumanAssociated Extension
MIxS Data that comply with the MimsMisip checklist and the HumanGut Extension
MIxS Data that comply with the MimsMisip checklist and the HumanOral Extension
MIxS Data that comply with the MimsMisip checklist and the HumanSkin Extension
MIxS Data that comply with the MimsMisip checklist and the HumanVaginal Extension
MimsMisip combined with MicrobialMatBiofilm
MIxS Data that comply with the MimsMisip checklist and the MicrobialMatBiofilm Extension
MimsMisip combined with MiscellaneousNaturalOrArtificialEnvironment
MIxS Data that comply with the MimsMisip checklist and the MiscellaneousNaturalOrArtificialEnvironment Extension
MIxS Data that comply with the MimsMisip checklist and the PlantAssociated Extension
MIxS Data that comply with the MimsMisip checklist and the Sediment Extension
MIxS Data that comply with the MimsMisip checklist and the Soil Extension
MimsMisip combined with WastewaterSludge
MIxS Data that comply with the MimsMisip checklist and the WastewaterSludge Extension
MIxS Data that comply with the MimsMisip checklist and the Water Extension
MimsMisip combined with HydrocarbonResourcesCores
MIxS Data that comply with the MimsMisip checklist and the HydrocarbonResourcesCores Extension
MimsMisip combined with HydrocarbonResourcesFluidsSwabs
MIxS Data that comply with the MimsMisip checklist and the HydrocarbonResourcesFluidsSwabs Extension
MIxS Data that comply with the MimsMisip checklist and the Agriculture Extension
MimsMisip combined with FoodAnimalAndAnimalFeed
MIxS Data that comply with the MimsMisip checklist and the FoodAnimalAndAnimalFeed Extension
MimsMisip combined with FoodFarmEnvironment
MIxS Data that comply with the MimsMisip checklist and the FoodFarmEnvironment Extension
MimsMisip combined with FoodFoodProductionFacility
MIxS Data that comply with the MimsMisip checklist and the FoodFoodProductionFacility Extension
MIxS Data that comply with the MimsMisip checklist and the FoodHumanFoods Extension
MimsMisip combined with SymbiontAssociated
MIxS Data that comply with the MimsMisip checklist and the SymbiontAssociated Extension
leafy greens-including fresh cut leafy greens
missing: data agreement established pre-2023
active surveillance in response to an outbreak
active surveillance not initiated by an outbreak
Data that comply with Extension Agriculture
Data that comply with Extension BuiltEnvironment
Data that comply with Extension FoodAnimalAndAnimalFeed
Data that comply with Extension FoodFarmEnvironment
Data that comply with Extension FoodFoodProductionFacility
Data that comply with Extension FoodHumanFoods
Data that comply with Extension HostAssociated
Data that comply with Extension HumanAssociated
Data that comply with Extension HumanGut
Data that comply with Extension HumanOral
Data that comply with Extension HumanSkin
Data that comply with Extension HumanVaginal
Data that comply with Extension HydrocarbonResourcesCores
Data that comply with Extension HydrocarbonResourcesFluidsSwabs
Data that comply with Extension MicrobialMatBiofilm
Data that comply with MigsBa combined with Agriculture
Data that comply with MigsBa combined with Air
Data that comply with MigsBa combined with BuiltEnvironment
Data that comply with MigsBa combined with FoodAnimalAndAnimalFeed
Data that comply with MigsBa combined with FoodFarmEnvironment
Data that comply with MigsBa combined with FoodFoodProductionFacility
Data that comply with MigsBa combined with FoodHumanFoods
Data that comply with MigsBa combined with HostAssociated
Data that comply with MigsBa combined with HumanAssociated
Data that comply with MigsBa combined with HumanGut
Data that comply with MigsBa combined with HumanOral
Data that comply with MigsBa combined with HumanSkin
Data that comply with MigsBa combined with HumanVaginal
Data that comply with MigsBa combined with HydrocarbonResourcesCores
MigsBaHydrocarbonResourcesFluidsSwabs data
Data that comply with MigsBa combined with HydrocarbonResourcesFluidsSwabs
Data that comply with MigsBa combined with MicrobialMatBiofilm
MigsBaMiscellaneousNaturalOrArtificialEnvironment data
Data that comply with MigsBa combined with MiscellaneousNaturalOrArtificialEnvironment
Data that comply with MigsBa combined with PlantAssociated
Data that comply with MigsBa combined with Sediment
Data that comply with MigsBa combined with Soil
Data that comply with MigsBa combined with SymbiontAssociated
Data that comply with MigsBa combined with WastewaterSludge
Data that comply with MigsBa combined with Water
Data that comply with MigsEu combined with Agriculture
Data that comply with MigsEu combined with Air
Data that comply with MigsEu combined with BuiltEnvironment
Data that comply with MigsEu combined with FoodAnimalAndAnimalFeed
Data that comply with MigsEu combined with FoodFarmEnvironment
Data that comply with MigsEu combined with FoodFoodProductionFacility
Data that comply with MigsEu combined with FoodHumanFoods
Data that comply with MigsEu combined with HostAssociated
Data that comply with MigsEu combined with HumanAssociated
Data that comply with MigsEu combined with HumanGut
Data that comply with MigsEu combined with HumanOral
Data that comply with MigsEu combined with HumanSkin
Data that comply with MigsEu combined with HumanVaginal
Data that comply with MigsEu combined with HydrocarbonResourcesCores
MigsEuHydrocarbonResourcesFluidsSwabs data
Data that comply with MigsEu combined with HydrocarbonResourcesFluidsSwabs
Data that comply with MigsEu combined with MicrobialMatBiofilm
MigsEuMiscellaneousNaturalOrArtificialEnvironment data
Data that comply with MigsEu combined with MiscellaneousNaturalOrArtificialEnvironment
Data that comply with MigsEu combined with PlantAssociated
Data that comply with MigsEu combined with Sediment
Data that comply with MigsEu combined with Soil
Data that comply with MigsEu combined with SymbiontAssociated
Data that comply with MigsEu combined with WastewaterSludge
Data that comply with MigsEu combined with Water
Data that comply with MigsOrg combined with Agriculture
Data that comply with MigsOrg combined with Air
Data that comply with MigsOrg combined with BuiltEnvironment
Data that comply with MigsOrg combined with FoodAnimalAndAnimalFeed
Data that comply with MigsOrg combined with FoodFarmEnvironment
Data that comply with MigsOrg combined with FoodFoodProductionFacility
Data that comply with MigsOrg combined with FoodHumanFoods
Data that comply with MigsOrg combined with HostAssociated
Data that comply with MigsOrg combined with HumanAssociated
Data that comply with MigsOrg combined with HumanGut
Data that comply with MigsOrg combined with HumanOral
Data that comply with MigsOrg combined with HumanSkin
Data that comply with MigsOrg combined with HumanVaginal
Data that comply with MigsOrg combined with HydrocarbonResourcesCores
MigsOrgHydrocarbonResourcesFluidsSwabs data
Data that comply with MigsOrg combined with HydrocarbonResourcesFluidsSwabs
Data that comply with MigsOrg combined with MicrobialMatBiofilm
MigsOrgMiscellaneousNaturalOrArtificialEnvironment data
Data that comply with MigsOrg combined with MiscellaneousNaturalOrArtificialEnvironment
Data that comply with MigsOrg combined with PlantAssociated
Data that comply with MigsOrg combined with Sediment
Data that comply with MigsOrg combined with Soil
Data that comply with MigsOrg combined with SymbiontAssociated
Data that comply with MigsOrg combined with WastewaterSludge
Data that comply with MigsOrg combined with Water
Data that comply with MigsPl combined with Agriculture
Data that comply with MigsPl combined with Air
Data that comply with MigsPl combined with BuiltEnvironment
Data that comply with MigsPl combined with FoodAnimalAndAnimalFeed
Data that comply with MigsPl combined with FoodFarmEnvironment
Data that comply with MigsPl combined with FoodFoodProductionFacility
Data that comply with MigsPl combined with FoodHumanFoods
Data that comply with MigsPl combined with HostAssociated
Data that comply with MigsPl combined with HumanAssociated
Data that comply with MigsPl combined with HumanGut
Data that comply with MigsPl combined with HumanOral
Data that comply with MigsPl combined with HumanSkin
Data that comply with MigsPl combined with HumanVaginal
Data that comply with MigsPl combined with HydrocarbonResourcesCores
MigsPlHydrocarbonResourcesFluidsSwabs data
Data that comply with MigsPl combined with HydrocarbonResourcesFluidsSwabs
Data that comply with MigsPl combined with MicrobialMatBiofilm
MigsPlMiscellaneousNaturalOrArtificialEnvironment data
Data that comply with MigsPl combined with MiscellaneousNaturalOrArtificialEnvironment
Data that comply with MigsPl combined with PlantAssociated
Data that comply with MigsPl combined with Sediment
Data that comply with MigsPl combined with Soil
Data that comply with MigsPl combined with SymbiontAssociated
Data that comply with MigsPl combined with WastewaterSludge
Data that comply with MigsPl combined with Water
Data that comply with MigsVi combined with Agriculture
Data that comply with MigsVi combined with Air
Data that comply with MigsVi combined with BuiltEnvironment
Data that comply with MigsVi combined with FoodAnimalAndAnimalFeed
Data that comply with MigsVi combined with FoodFarmEnvironment
Data that comply with MigsVi combined with FoodFoodProductionFacility
Data that comply with MigsVi combined with FoodHumanFoods
Data that comply with MigsVi combined with HostAssociated
Data that comply with MigsVi combined with HumanAssociated
Data that comply with MigsVi combined with HumanGut
Data that comply with MigsVi combined with HumanOral
Data that comply with MigsVi combined with HumanSkin
Data that comply with MigsVi combined with HumanVaginal
Data that comply with MigsVi combined with HydrocarbonResourcesCores
MigsViHydrocarbonResourcesFluidsSwabs data
Data that comply with MigsVi combined with HydrocarbonResourcesFluidsSwabs
Data that comply with MigsVi combined with MicrobialMatBiofilm
MigsViMiscellaneousNaturalOrArtificialEnvironment data
Data that comply with MigsVi combined with MiscellaneousNaturalOrArtificialEnvironment
Data that comply with MigsVi combined with PlantAssociated
Data that comply with MigsVi combined with Sediment
Data that comply with MigsVi combined with Soil
Data that comply with MigsVi combined with SymbiontAssociated
Data that comply with MigsVi combined with WastewaterSludge
Data that comply with MigsVi combined with Water
Data that comply with Mimag combined with Agriculture
Data that comply with Mimag combined with Air
Data that comply with Mimag combined with BuiltEnvironment
Data that comply with Mimag combined with FoodAnimalAndAnimalFeed
Data that comply with Mimag combined with FoodFarmEnvironment
Data that comply with Mimag combined with FoodFoodProductionFacility
Data that comply with Mimag combined with FoodHumanFoods
Data that comply with Mimag combined with HostAssociated
Data that comply with Mimag combined with HumanAssociated
Data that comply with Mimag combined with HumanGut
Data that comply with Mimag combined with HumanOral
Data that comply with Mimag combined with HumanSkin
Data that comply with Mimag combined with HumanVaginal
Data that comply with Mimag combined with HydrocarbonResourcesCores
MimagHydrocarbonResourcesFluidsSwabs data
Data that comply with Mimag combined with HydrocarbonResourcesFluidsSwabs
Data that comply with Mimag combined with MicrobialMatBiofilm
MimagMiscellaneousNaturalOrArtificialEnvironment data
Data that comply with Mimag combined with MiscellaneousNaturalOrArtificialEnvironment
Data that comply with Mimag combined with PlantAssociated
Data that comply with Mimag combined with Sediment
Data that comply with Mimag combined with Soil
Data that comply with Mimag combined with SymbiontAssociated
Data that comply with Mimag combined with WastewaterSludge
Data that comply with Mimag combined with Water
Data that comply with MimarksC combined with Agriculture
Data that comply with MimarksC combined with Air
Data that comply with MimarksC combined with BuiltEnvironment
Data that comply with checklist MimarksC
Data that comply with MimarksC combined with FoodAnimalAndAnimalFeed
Data that comply with MimarksC combined with FoodFarmEnvironment
Data that comply with MimarksC combined with FoodFoodProductionFacility
Data that comply with MimarksC combined with FoodHumanFoods
Data that comply with MimarksC combined with HostAssociated
Data that comply with MimarksC combined with HumanAssociated
Data that comply with MimarksC combined with HumanGut
Data that comply with MimarksC combined with HumanOral
Data that comply with MimarksC combined with HumanSkin
Data that comply with MimarksC combined with HumanVaginal
Data that comply with MimarksC combined with HydrocarbonResourcesCores
MimarksCHydrocarbonResourcesFluidsSwabs data
Data that comply with MimarksC combined with HydrocarbonResourcesFluidsSwabs
Data that comply with MimarksC combined with MicrobialMatBiofilm
MimarksCMiscellaneousNaturalOrArtificialEnvironment data
Data that comply with MimarksC combined with MiscellaneousNaturalOrArtificialEnvironment
Data that comply with MimarksC combined with PlantAssociated
Data that comply with MimarksC combined with Sediment
Data that comply with MimarksC combined with Soil
Data that comply with MimarksC combined with SymbiontAssociated
Data that comply with MimarksC combined with WastewaterSludge
Data that comply with MimarksC combined with Water
Data that comply with MimarksS combined with Agriculture
Data that comply with MimarksS combined with Air
Data that comply with MimarksS combined with BuiltEnvironment
Data that comply with checklist MimarksS
Data that comply with MimarksS combined with FoodAnimalAndAnimalFeed
Data that comply with MimarksS combined with FoodFarmEnvironment
Data that comply with MimarksS combined with FoodFoodProductionFacility
Data that comply with MimarksS combined with FoodHumanFoods
Data that comply with MimarksS combined with HostAssociated
Data that comply with MimarksS combined with HumanAssociated
Data that comply with MimarksS combined with HumanGut
Data that comply with MimarksS combined with HumanOral
Data that comply with MimarksS combined with HumanSkin
Data that comply with MimarksS combined with HumanVaginal
Data that comply with MimarksS combined with HydrocarbonResourcesCores
MimarksSHydrocarbonResourcesFluidsSwabs data
Data that comply with MimarksS combined with HydrocarbonResourcesFluidsSwabs
Data that comply with MimarksS combined with MicrobialMatBiofilm
MimarksSMiscellaneousNaturalOrArtificialEnvironment data
Data that comply with MimarksS combined with MiscellaneousNaturalOrArtificialEnvironment
Data that comply with MimarksS combined with PlantAssociated
Data that comply with MimarksS combined with Sediment
Data that comply with MimarksS combined with Soil
Data that comply with MimarksS combined with SymbiontAssociated
Data that comply with MimarksS combined with WastewaterSludge
Data that comply with MimarksS combined with Water
MimsMisipFoodFoodProductionFacility data
Data that comply with MimsMisip combined with FoodFoodProductionFacility
Data that comply with Mims combined with Agriculture
Data that comply with Mims combined with Air
Data that comply with Mims combined with BuiltEnvironment
Data that comply with Mims combined with FoodAnimalAndAnimalFeed
Data that comply with Mims combined with FoodFarmEnvironment
Data that comply with Mims combined with FoodFoodProductionFacility
Data that comply with Mims combined with FoodHumanFoods
Data that comply with Mims combined with HostAssociated
Data that comply with Mims combined with HumanAssociated
Data that comply with Mims combined with HumanGut
Data that comply with Mims combined with HumanOral
Data that comply with Mims combined with HumanSkin
Data that comply with Mims combined with HumanVaginal
Data that comply with Mims combined with HydrocarbonResourcesCores
MimsHydrocarbonResourcesFluidsSwabs data
Data that comply with Mims combined with HydrocarbonResourcesFluidsSwabs
Data that comply with Mims combined with MicrobialMatBiofilm
MimsMiscellaneousNaturalOrArtificialEnvironment data
Data that comply with Mims combined with MiscellaneousNaturalOrArtificialEnvironment
Data that comply with Mims combined with PlantAssociated
Data that comply with Mims combined with Sediment
Data that comply with Mims combined with Soil
Data that comply with Mims combined with SymbiontAssociated
Data that comply with Mims combined with WastewaterSludge
Data that comply with Mims combined with Water
Data that comply with MimsMisip combined with Agriculture
Data that comply with MimsMisip combined with Air
Data that comply with MimsMisip combined with BuiltEnvironment
Data that comply with checklist MimsMisip
Data that comply with MimsMisip combined with FoodAnimalAndAnimalFeed
Data that comply with MimsMisip combined with FoodFarmEnvironment
Data that comply with MimsMisip combined with FoodHumanFoods
Data that comply with MimsMisip combined with HostAssociated
Data that comply with MimsMisip combined with HumanAssociated
Data that comply with MimsMisip combined with HumanGut
Data that comply with MimsMisip combined with HumanOral
Data that comply with MimsMisip combined with HumanSkin
Data that comply with MimsMisip combined with HumanVaginal
Data that comply with MimsMisip combined with HydrocarbonResourcesCores
MimsMisipHydrocarbonResourcesFluidsSwabs data
Data that comply with MimsMisip combined with HydrocarbonResourcesFluidsSwabs
Data that comply with MimsMisip combined with MicrobialMatBiofilm
MimsMisipiscellaneousNaturalOrArtificialEnvironment data
Data that comply with MimsMisip combined with MiscellaneousNaturalOrArtificialEnvironment
Data that comply with MimsMisip combined with PlantAssociated
Data that comply with MimsMisip combined with Sediment
Data that comply with MimsMisip combined with Soil
Data that comply with MimsMisip combined with SymbiontAssociated
Data that comply with MimsMisip combined with WastewaterSludge
Data that comply with MimsMisip combined with Water
Data that comply with Misag combined with Agriculture
Data that comply with Misag combined with Air
Data that comply with Misag combined with BuiltEnvironment
Data that comply with Misag combined with FoodAnimalAndAnimalFeed
Data that comply with Misag combined with FoodFarmEnvironment
Data that comply with Misag combined with FoodFoodProductionFacility
Data that comply with Misag combined with FoodHumanFoods
Data that comply with Misag combined with HostAssociated
Data that comply with Misag combined with HumanAssociated
Data that comply with Misag combined with HumanGut
Data that comply with Misag combined with HumanOral
Data that comply with Misag combined with HumanSkin
Data that comply with Misag combined with HumanVaginal
Data that comply with Misag combined with HydrocarbonResourcesCores
MisagHydrocarbonResourcesFluidsSwabs data
Data that comply with Misag combined with HydrocarbonResourcesFluidsSwabs
Data that comply with Misag combined with MicrobialMatBiofilm
MisagMiscellaneousNaturalOrArtificialEnvironment data
Data that comply with Misag combined with MiscellaneousNaturalOrArtificialEnvironment
Data that comply with Misag combined with PlantAssociated
Data that comply with Misag combined with Sediment
Data that comply with Misag combined with Soil
Data that comply with Misag combined with SymbiontAssociated
Data that comply with Misag combined with WastewaterSludge
Data that comply with Misag combined with Water
MiscellaneousNaturalOrArtificialEnvironment data
Data that comply with Extension MiscellaneousNaturalOrArtificialEnvironment
Data that comply with Miuvig combined with Agriculture
Data that comply with Miuvig combined with Air
Data that comply with Miuvig combined with BuiltEnvironment
Data that comply with Miuvig combined with FoodAnimalAndAnimalFeed
Data that comply with Miuvig combined with FoodFarmEnvironment
Data that comply with Miuvig combined with FoodFoodProductionFacility
Data that comply with Miuvig combined with FoodHumanFoods
Data that comply with Miuvig combined with HostAssociated
Data that comply with Miuvig combined with HumanAssociated
Data that comply with Miuvig combined with HumanGut
Data that comply with Miuvig combined with HumanOral
Data that comply with Miuvig combined with HumanSkin
Data that comply with Miuvig combined with HumanVaginal
Data that comply with Miuvig combined with HydrocarbonResourcesCores
MiuvigHydrocarbonResourcesFluidsSwabs data
Data that comply with Miuvig combined with HydrocarbonResourcesFluidsSwabs
Data that comply with Miuvig combined with MicrobialMatBiofilm
MiuvigMiscellaneousNaturalOrArtificialEnvironment data
Data that comply with Miuvig combined with MiscellaneousNaturalOrArtificialEnvironment
Data that comply with Miuvig combined with PlantAssociated
Data that comply with Miuvig combined with Sediment
Data that comply with Miuvig combined with Soil
Data that comply with Miuvig combined with SymbiontAssociated
Data that comply with Miuvig combined with WastewaterSludge
Data that comply with Miuvig combined with Water
Data that comply with Extension PlantAssociated
Data that comply with Extension Sediment
Data that comply with Extension SymbiontAssociated
Data that comply with Extension WastewaterSludge
The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO
Type of dataset from which the UViG was obtained
Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used
software name, version and relevant parameters
Cutoffs and approach used when clustering species-level OTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside OTUs defined from another set of thresholds, even if the latter are the ones primarily used during the analysis
Tool and thresholds used to compare sequences when computing "species-level" OTUs
Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" OTUs, if any
Tool or approach used for host prediction
For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature
Force per unit area exerted against a surface by the weight of air above that surface
Carbon monoxide (gas) amount or concentration at the time of sampling
Oxygen (gas) amount or concentration at the time of sampling
Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air
Actual mass of water vapor present in the air water vapor mixture.
Can be calculated via mass of water vapor divided by the volume of the air and water vapor mixture.
gram per gram, kilogram per kilogram, kilogram, pound, gram per cubic meter, kilogram per cubic meter, percent
Surfaces: water activity as a function of air and material moisture
Temperature of the surface at the time of sampling
parts per million, gram per cubic meter, gram per square meter
The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water
Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays
The unit of illuminance and luminous emittance, measuring luminous flux per unit area
The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day
The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day
The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow
The amount of exposed ductwork in the room
The age of the built structure since construction
The area of the ceiling space within the room
The time period since installment of the carpet or flooring
The area of the floor space within the room
The ability of the floor to provide inertia against temperature fluctuations
The average carpet fiber height in the indoor environment
The recorded value at sampling time (power density)
The rate at which outside air replaces indoor air in a given space
The number of exterior doors in the built structure
The recorded outside relative humidity value at the time of sampling
Distance between doors (meters) in the hallway between the sampling room and adjacent rooms
The net floor area of sampling room. Net area excludes wall thicknesses
The recent and long term history of outside sampling
The recorded temperature value at sampling time outside
The total area of the sampled room's walls
The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound
Type of wastewater treatment plant as municipial or industrial
Average number of occupants at time of sampling per square footage
The street name and building number where the sampling occurred
List of rooms (room number, room name) immediately adjacent to the sampling room
The average height of the walls in the sampled room
The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint
The number of floors in the building, including basements and mechanical penthouse
The number of times a meal is cooked per week
The total count of hallways and corridors in the built structure
The maximum amount of people allowed in the indoor environment
The number of plant(s) in the sampling space
The number of pets residing in the sampled space
The number of individuals currently occupying in the sampling location
The unique details and component parts that, together, form the architecture of a distinguishable space within a built structure
The total count of rooms in the built structure including all room types
The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed
Count of room occupancy at time of sampling
List of room(s) (room number, room name) located in the same hallway as sampling room
rooms that share a door with sampling room
List of room(s) (room number, room name) sharing a door with the sampling room
rooms that share a wall with sampling room
List of room(s) (room number, room name) sharing a wall with the sampling room
The material the shading device is composed of
The number of times windows are opened per week
Taxonomic information about the host below subspecies level
Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc
Resting diastolic blood pressure, measured as mm mercury
Resting systolic blood pressure, measured as mm mercury
HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO]
Specification of major diet changes in the last six months, if yes the change should be specified
Specification of the maternal health status
Specification of foetal health status, should also include abortion
Specification of the color of the amniotic fluid sample
Current sexual partner and frequency of sex
Specification of birth control medication used
Specification of whether hysterectomy was performed
Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss
weight loss specification;measurement value
Reference or method used in determining the water content of soil
extreme_unusual_properties/Al saturation method
Reference or method used in determining Al saturation
Link to additional analysis results performed on the sample
The process of pre-treatment removes materials that can be easily collected from the raw wastewater
The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed
Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage
The process for substantially degrading the biological content of the sewage
The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment
The origin of wastewater such as human waste, rainfall, storm drains, etc
Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))
Depth of the original oil water contact (OWC) zone (average) (m TVDSS)
Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m
measurement value or measurement value range
In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field
Oil and/or gas production rates per well (e.g. 524 m3 / day)
Water production rates per well (e.g. 987 m3 / day)
Current amount of water (%) in a produced fluid stream; or the average of the combined streams
Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)
Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)
measurement value;frequency;duration;duration
Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)
Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)
Information about treatment(s) involving exposure to light, including both light intensity and quality
exposure type;light intensity;light quality
Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5 mg/L)
Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA
extreme_unusual_properties/Al saturation
Aluminum saturation (esp. For tropical soils)
Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period
A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite
Percentage of volatile solids removed from the anaerobic digestor
Percentage of industrial effluents received by wastewater treatment plant
The time activated sludge remains in reactor
Bacterial production in the water column measured by isotope uptake
Measurement of bacterial respiration in the water column
milligram per cubic meter per day, micromole oxygen per liter per hour
Concentration of dissolved inorganic nitrogen
microgram per liter, micromole per liter
Visible waveband radiance and irradiance measurements in the water column
microEinstein per square meter per second, microEinstein per square centimeter per second
milligram chlorophyll a per cubic meter, volts
Concentration of particulate organic nitrogen
A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads
number of photons per second per unit area
Measurement of primary production, generally measured as isotope uptake
milligram per cubic meter per day, gram per square meter per day
Concentration of soluble reactive phosphorus
micromole per liter, milligram per liter, parts per million
Concentration of suspended particulate matter
Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen
A distinguishable space within a structure, the purpose for which discrete areas of a building is used
A location (geography) where a building is set
Customary or normal density of occupants
Number of occupants present at time of sample within the given space
Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together
An architectural structure is a human-made, free-standing, immobile outdoor construction
The characterization of the location of the built structure as high or low human density
The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
The type of material used to finish a ceiling
Signs of the presence of mold or mildew on the ceiling
The feel, appearance, or consistency of a ceiling surface
The type of ceiling according to the ceiling's appearance or construction
design, construction, and operation documents
The building design, construction and operation documents
The relative location of the door in the room
Signs of the presence of mold or mildew on a door
The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents
The number of elevators within the built structure
The number of escalators within the built structure
The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
The floor covering type; the finished surface that is walked on
Signs of the presence of mold or mildew in a room
Refers to the structural elements and subfloor upon which the finish flooring is installed
The types of furniture present in the sampled room
The handidness of the individual sampled
The location of heat delivery within the room
The method by which the heat is delivered through the system
The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
The last time the floor was cleaned (swept, mopped, vacuumed)
mechanical structure: a moving structure
The compass direction the exterior window of the room is facing
The quadrant position of the sampling room within the building
The sampling location within the train car
The condition of the room at the time of sampling
The position of the room within the building
The horizontal sampling position in the room relative to architectural elements
The main purpose or activity of the sampling room. A room is any distinguishable space within a structure
List of rooms connected to the sampling room by a doorway
The physical condition of the shading device at the time of sampling
The location of the shading device in relation to the built structure
Signs of the presence of mold or mildew on the shading device
The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents
The building class of the wall defined by the composition of the building elements and fire-resistance rating
The material utilized to finish the outer most layer of the wall
The relative location of the wall within the room
Signs of the presence of mold or mildew on a wall
The feel, appearance, or consistency of a wall surface
The type of water feature present within the building being sampled
The day of the week when sampling occurred
The physical condition of the window at the time of sampling
The horizontal position of the window on the wall
The relative location of the window within the room
The type of material used to finish a window
Signs of the presence of mold or mildew on the window
Defines whether the windows were open or closed during environmental testing
The vertical position of the window on the wall
sex of the symbiotic organism (host of the samples); enumeration
Specification of study completion status, if no the reason should be specified
YES or NO due to (1)adverse event (2) non-compliance (3) lost to follow up (4)other-specify
Specification of urine collection method
Specification of the time since last toothbrushing
Specification of the time since last wash
Whether subject had hormone replacement theraphy, and if yes start date
Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field
Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field
Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field
Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field
secondary and tertiary recovery methods and start date
Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field
injection water breakthrough date of specific well
Injection water breakthrough date per well following a secondary and/or tertiary recovery
List of biocides (commercial name of product and supplier) and date of administration
List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included
Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field
Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors
Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research
Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite
Specification of the solidifying agent in the culture rooting medium; e.g. agar
Description of plant tissue culture growth media used
Information about the sediment type based on major constituents
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
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)
The number of times farm equipment is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually
Date of administration of soil amendment or fertilizer. Multiple terms may apply and can be separated by pipes, listing in reverse chronological order
Porosity of soil or deposited sediment is volume of voids divided by the total volume of sample
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
Number of water delivery events within a given period of time
The process of cleaning food to separate other environmental materials from the food source. Multiple terms can be separated by pipes
The amount of headspace oxygen in a fermentation vessel
The growth medium used for the fermented food fermentation process, which supplies the required nutrients. Usually this includes a carbon and nitrogen source, water, micronutrients and chemical additives
The pH of the fermented food fermentation process
The relative humidity of the fermented food fermentation process
The temperature of the fermented food fermentation process
The time duration of the fermented food fermentation process
The type of vessel used for containment of the fermentation
Any type of microorganisms used in food production. This field accepts terms listed under live organisms for food production (http://purl.obolibrary.org/obo/FOODON_0344453)
Total cell count of starter culture per gram, volume or area of sample and the method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) should also be provided. (example : total prokaryotes; 3.5e7 cells per ml; qPCR)
organism name; measurement value; enumeration
colony forming units per milliliter; colony forming units per gram of dry weight
The amount of starter culture used to inoculate a new batch
Information about the protocol or method used to prepare the starter inoculum
The source from which the microbial starter culture was sourced. If commercially supplied, list supplier
Please include Genus species and strain ID, if known of microorganisms used in food production. For complex communities, pipes can be used to separate two or more microbes
The name(s) (generic or brand) of the antimicrobial(s) given to the food animal within the last 30 days
The duration of time (days) that the antimicrobial was administered to the food animal
The frequency per day that the antimicrobial was administered to the food animal
food animal antimicrobial route of administration
The route by which the antimicrobial is administered into the body of the food animal
The prescribed intended use of or the condition treated by the antimicrobial given to the food animal by any route of administration
Body condition scoring is a production management tool used to evaluate overall health and nutritional needs of a food animal. Because there are different scoring systems, this field is restricted to three categories
The sex and reproductive status of the food animal
The age of the food source host organism. Depending on the type of host organism, age may be more appropriate to report in days, weeks, or years
The subdivision of areas within a food production facility according to hygienic requirements. This field accepts terms listed under hygienic food production area (http://purl.obolibrary.org/obo/ENVO). Please add a term that most accurately indicates the hygienic area your sample was taken from according to the definitions provided
food production environmental monitoring zone
An environmental monitoring zone is a formal designation as part of an environmental monitoring program, in which areas of a food production facility are categorized, commonly as zones 1-4, based on likelihood or risk of foodborne pathogen contamination. This field accepts terms listed under food production environmental monitoring zone (http://purl.obolibrary.org/obo/ENVO). Please add a term to indicate the environmental monitoring zone the sample was taken from
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected
The condition of the sample location at the time of sampling
Measurement of photosythetic activity (i.e. leaf gas exchange / chlorophyll fluorescence emissions / reflectance / transpiration) Please also include the term method term detailing the method of activity measurement
Time spent in host of the symbiotic organism at the time of sampling; relevant scale depends on symbiotic organism and study
Type of life cycle of the symbiotic host species (the thing being sampled). Simple life cycles occur within a single host, complex ones within multiple different hosts over the course of their normal life cycle
type of life cycle of the symbiotic organism (host of the samples)
Role of the host in the life cycle of the symbiotic organism
Number of symbiotic host individuals pooled at the time of collection
NCBI taxon id of the host of the symbiotic host organism
NCBI taxon identifier of the host of the symbiotic taxon organism
Type of biological interaction established between the symbiotic host organism being sampled and its respective host
Level of specificity of symbiont-host interaction: e.g. generalist (symbiont able to establish associations with distantly related hosts) or species-specific
observed coinfecting organisms in host of host
The taxonomic name of any coinfecting organism observed in a symbiotic relationship with the host of the sampled host organism. e.g. where a sample collected from a host trematode species (A) which was collected from a host_of_host fish (B) that was also infected with a nematode (C), the value here would be (C) the nematode {species name} or {common name}. Multiple co-infecting species may be added in a comma-separated list. For listing symbiotic organisms associated with the host (A) use the term Observed host symbiont
The process through which the symbiotic host organism entered the host from which it was sampled
The localization of the symbiotic host organism within the host from which it was sampled: e.g. intracellular if the symbiotic host organism is localized within the cells or extracellular if the symbiotic host organism is localized outside of cells
Type of host dependence for the symbiotic host organism to its host
Description of path taken by the symbiotic host organism being sampled in order to establish a symbiotic relationship with the host (with which it was observed at the time of sampling) via a mode of transmission (specified in mode_transmission)
Solution within which sample was stored, if any
Common name of the host of the symbiotic host organism
host of the symbiotic host environmental medium
Report the environmental material(s) immediately surrounding the symbiotic host organism at the time of sampling. This usually will be a tissue or substance type from the host, but may be another material if the symbiont is external to the host. We recommend using classes from the UBERON ontology, but subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483) may also be used. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. intestines, heart).MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. intestines, heart)
An ontology term for a material such as a tissue type or excreted substance
A unique identifier by which each host of the symbiotic host organism subject can be referred to, de-identified, e.g. #H14
host of the symbiotic host infra-specific name
Taxonomic name information of the host of the symbiotic host organism below subspecies level
host of the symbiotic host infra-specific rank
Taxonomic rank information about the host of the symbiotic host organism below subspecies level, such as variety, form, rank etc
Observed genotype of the host of the symbiotic host organism
Phenotype of the host of the symbiotic host organism. For phenotypic quality ontology (PATO) terms, see http://purl.bioontology.org/ontology/pato
phenotype of the host of the symbiotic organism; PATO
Whether or not the host of the symbiotic host organism is gravid, and if yes date due or date post-conception, specifying which is used
Total mass of the host of the symbiotic host organism at collection, the unit depends on the host
List whether the isotopologue added to this biological sample was heavy-labelled or natural abundance
Labeling approach (number of labeled isotopologs supplied)
The labelling approach of this SIP experiment. Details if multiple isotopically labelled isotopologues were added to samples ("multiple"), or was only one isotopologue added to each sample ("single").
A number designating the gradient position from heaviest (=1) to lightest. Unfractionated samples, from which fractionated samples were derived, should be denoted with –1.
relative amount of nucleic acids in the gradient position
The total nucleic acids loaded onto the column in this fraction as a decimal. If uploading 16S rRNA gene (or other amplicon) sequencing data, this value should be calculated from qPCR data. If uploading untargetted sequencing data, this value should be calculated from total DNA concentration.
Method used to fractionate nucleic acids.
The fraction of heavy-labelled atoms out of all atoms of a given element in the isotopolog. Multiple values allowed, separated by a | and should be orded the same as the isotopolog.
InChI label designating set of all isotopically enriched atoms in isotopologue. Multiple values allowed, separated by a | and should be orded the same as the isotopolog.
The concentration (in ppm) of isotopolog added to environmental matrix as a total mass per volume.
isotopolog mass / total volume soil; ppm of isotopologue in total container volume
Excess atom fraction of the nucleobases in this fraction.
Total time of incubation after isotopologue addition in hours
Method used for internal standard for SIP fractionation, if an internal standard was used (i.e., spiking in a heavy-labelled DNA sequence).
DNA concentration of sample after dna extraction prior to pooling. Typically measured spectrophotometrically or with a fluorophore.
Volume the nucleic acid (DNA or RNA) sample is eluted in
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
Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens
Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens
Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens
Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens
Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens
gram, microgram, mole per liter, gram per liter
Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
Addition of fertilizers, pesticides, etc. - amount and time of applications
Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi
Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates
Information about any mechanical damage exerted on the plant; can include multiple damages and sites
Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen
Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment
Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
Description of the feeding equipment used for livestock. This field accepts terms listed under feed delivery (http://opendata.inra.fr/EOL/EOL_0001757). Multiple terms can be separated by pipes
Description of the equipment or method used to distribute water to livestock. This field accepts termed listed under water delivery equipment (http://opendata.inra.fr/EOL/EOL_0001653). Multiple terms can be separated by pipes
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
List of planting, growing or harvesting equipment shared with other farms. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes
Method used to sanitize growing and harvesting equipment. This can including type and concentration of sanitizing solution. Multiple terms can be separated by one or more pipes
text or commercial name of sanitizer or class of sanitizer or active ingredient in sanitizer
List of equipment used for planting, fertilization, harvesting, irrigation, land levelling, residue management, weeding or transplanting during the growing season. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes
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
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
Descriptors of the food production system such as wild caught, free-range, organic, free-range, industrial, dairy, beef
Other users sharing access to the same water source. Multiple terms can be separated by one or more pipes
Description of the housing system of the livestock. This field accepts terms listed under terrestrial management housing system (http://opendata.inra.fr/EOL/EOL_0001605)
These descriptors are used either for foods intended for special dietary use as defined in 21 CFR 105 or for foods that have special characteristics indicated in the name or labeling. This field accepts terms listed under dietary claim or use (http://purl.obolibrary.org/obo/FOODON_03510023). Multiple terms can be separated by one or more pipes, but please consider limiting this list to the most prominent dietary claim or use
A label indication that the product contains a recognized allergen. This field accepts terms listed under dietary claim or use (http://purl.obolibrary.org/obo/FOODON_03510213)
food distribution point geographic location (city)
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
The name of the extraction kit used to recover the nucleic acid fraction of an input material is performed
antimicrobial phenotype of spike-in bacteria
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)
Labeling claims containing descriptors such as wild caught, free-range, organic, free-range, industrial, hormone-free, antibiotic free, cage free. Can include more than one term, separated by ";"
Kit used to amplify genomic DNA in preparation for sequencing
List of approaches used to enrich the sample for viruses, if any
single cell or viral particle lysis kit protocol
Name of the kit or standard protocol used for cell(s) or particle(s) lysis
Method used to amplify genomic DNA in preparation for sequencing
Can a 16S gene be recovered from the submitted SAG or MAG?
The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases
Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer
Method used to sort/isolate cells or particles of interest
single cell or viral particle lysis approach
Method used to free DNA from interior of the cell(s) or particle(s)
The parameters that have been applied during the extraction of genomes from metagenomic datasets
Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used
Has an assembly been performed on a genome bin extracted from a metagenomic assembly?
Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets
Carbon dioxide (gas) amount or concentration at the time of sampling
If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)
gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles
number of cells per gram (or ml or cm^2)
Concentration of total iron in the sample
milligram per liter, milligram per kilogram
The amount of solar energy that arrives at a specific area of a surface during a specific time interval
kilowatts per square meter per day, ergs per square centimeter per second
Ventilation rate of the system in the sampled premises
cubic meter per minute, liters per second
speed of wind measured at the time of sampling
Total Acid Number (TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)
Temperature of the air at the time of sampling
A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 °C)
Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (source: https://en.wikipedia.org/wiki/pour_point)
Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
Concentration of dissolved iron in the sample
Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances
gram, microgram, milligram per liter, mole per liter, gram per liter, part per million
Concentration of Volatile Fatty Acids in the sample
Concentration of ethylbenzene in the sample
API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1 API)
Concentration of phaeopigments; can include multiple phaeopigments
The length, width and height of sampling room
Measurement of magnitude and direction of flow within a fluid
The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually
Sampling room number. This ID should be consistent with the designations on the building floor plans
Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen
Name of the hydrocarbon field (e.g. Albacora)
Name of the well (e.g. BXA1123) where sample was taken
A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)
Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary
Vegetation classification from one or more standard classification systems, or agricultural crop
Reference or method used in vegetation classification
Reference or method used in determining previous land use and dates
Historical and/or physical evidence of flooding
Unusual physical events that may have affected microbial populations
Reference or method used in determining the horizon
Collection design of pooled samples and/or sieve size and amount of sample sieved
Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)
Link to digitized soil maps or other soil classification information
Soil classification based on local soil classification system
soil_taxonomic/local classification method
Reference or method used in determining the local soil classification
The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional
Reference or method used in determining microbial biomass
slot name/scn was microbial_biomass_meth
extreme_unusual_properties/heavy metals method
Reference or method used in determining heavy metals
hydrocarbon resource original temperature
Original temperature of the hydrocarbon resource
depth (TVDSS) of hydrocarbon resource temperature
True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m)
Original pressure of the hydrocarbon resource
depth (TVDSS) of hydrocarbon resource pressure
True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m)
Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS
Original sulfate concentration in the hydrocarbon resource
Original volatile fatty acid concentration in the hydrocarbon resource
Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 C)
Concentration of total sulfur in the sample
Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxygen-corrosion and microbial activity (e.g. Mic)
micromole per kilogram, milligram per liter
Concentration of n-alkanes; can include multiple n-alkanes
Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L)
Measurement of total depth of water column
The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps
Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer
The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration
The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units
Total amount or concentration of phosphate
Ventilation system used in the sampled premises
Wind direction is the direction from which a wind originates
Surface materials at the point of sampling
Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room
The type and number of animals or insects present in the sampling space
The floor of the building, where the sampling room is located
Original body habitat where the sample was obtained from
Literature reference giving growth conditions of the host
Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used
Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field
Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field
Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field
Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field
Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field
Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field
Characteristic shape, appearance or growth form of a plant species
Substance produced by the plant, where the sample was obtained from
Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here
Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container
Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath
Soil classification from the FAO World soil distribution from International Soil Reference and Information Centre (ISRIC). The list of available soil classifications can be found at https://www.isric.org/explore/world-soil-distribution
Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas
Drainage classification from a standard system such as the USDA system
Historical and/or physical evidence of fire
Source of water used on the farm for irrigation of crops or watering of livestock
Description of the equipment or method used to distribute water to crops. This field accepts termed listed under irrigation process (http://purl.obolibrary.org/obo/AGRO_00000006). Multiple terms can be separated by pipes
Amount of crop produced per unit or area of land
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 accepts 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
The number of food animals of the same species that are maintained together as a unit, i.e. a herd or flock
Average humidity of the region throughout the growing season
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
Soil electrical conductivity (EC) is a measure of how well soil water can carry an electrical current. Electrical conductivity of soil solution is a reliable indicator of its solute (cation or anion) concentration with 1 dS/m approximately equivalent to 10 meq/L (U.S. Salinity Laboratory Staff, 1954).
Material covering the sampled soil. This field accepts terms under ENVO:00010483, environmental material
subclass of 'environmental material', http://purl.obolibrary.org/obo/ENVO_00010483
pH measurement of some soil at the time of sampling
Location of sampled soil to other parts of the farm e.g. under crop plant, near irrigation ditch, from the dirt road
Temperature of soil at the time of sampling
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
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
NCIT:C14250 or antigenic formula or serovar name
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
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
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
heavy metal name or chemical symbol; concentration
pH measurement of some water at the time of sampling
food stored by consumer (storage duration)
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)
Temperature at which food commodity was stored by the consumer, prior to onset of illness or sample collection
The date a food product was purchased by consumer
The quantity of food purchased by consumer
A substance or substances added to food to maintain or improve safety and freshness, to improve or maintain nutritional value, or improve taste, texture and appearance. This field accepts terms listed under food additive (http://purl.obolibrary.org/obo/FOODON_03412972). Multiple terms can be separated by one or more pipes, but please consider limiting this list to the top 5 ingredients listed in order as on the food label. See also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors
The transformation of raw food by the application of heat. This field accepts terms listed under food cooking (http://purl.obolibrary.org/obo/FOODON_03450002)
food distribution point geographic location
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
A datum indicating that use of a food product name is regulated in some legal jurisdiction. This field accepts terms listed under food product name legal status (http://purl.obolibrary.org/obo/FOODON_03530087)
A term label and term id to describe the state of the packing material and text to explain the exact condition. This field accepts terms listed under food packing medium integrity (http://purl.obolibrary.org/obo/FOODON_03530218)
material of contact prior to food packaging
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
Other names by which the food product is known by (e.g., regional or non-English names)
Hazard Analysis Critical Control Points (HACCP) guide food safety term
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)
The number of samples collected during the current sampling event
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. This field accepts terms under study design (http://purl.obolibrary.org/obo/OBI_0500000). If the proper descriptor is not listed please use text to describe the study design. Multiple terms can be separated by pipes
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
Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements
Concentration of diether lipids; can include multiple types of diether lipids
Concentration of phospholipid fatty acids; can include multiple values
phospholipid fatty acid name;measurement value
Taxonomic information about the cultured organism(s)
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
NCIT:C14250 or NCBI taxid or culture independent
The specific container or coating materials in direct contact with the food. Multiple values can be assigned. This field accepts terms listed under food contact surface (http://purl.obolibrary.org/obo/FOODON_03500010)
The medium in which the food is packed for preservation and handling or the medium surrounding homemade foods, e.g., peaches cooked in sugar syrup. The packing medium may provide a controlled environment for the food. It may also serve to improve palatability and consumer appeal. This includes edible packing media (e.g. fruit juice), gas other than air (e.g. carbon dioxide), vacuum packed, or packed with aerosol propellant. This field accepts terms under food packing medium (http://purl.obolibrary.org/obo/FOODON_03480020). Multiple terms may apply and can be separated by pipes
The methods contributing to the prevention or retardation of microbial, enzymatic or oxidative spoilage and thus to the extension of shelf life. This field accepts terms listed under food preservation process (http://purl.obolibrary.org/obo/FOODON_03470107)
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)
Food consumer type, human or animal, for which the food product is produced and marketed. This field accepts terms listed under food consumer group (http://purl.obolibrary.org/obo/FOODON_03510136) or NCBI taxid
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)
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
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
Interagency Food Safety Analytics Collaboration (IFSAC) category
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
Descriptors of the food production system or of the agricultural environment and growing conditions related to the farm production system, such as wild caught, organic, free-range, industrial, dairy, beef, domestic or cultivated food production. This field accepts terms listed under food production (http://purl.obolibrary.org/obo/FOODON_03530206). Multiple terms may apply and can be separated by pipes
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
Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar
Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote
for eukaryotes and bacteria: chromosomes (haploid count); for viruses: segments
The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual
for virus: lytic, lysogenic, temperate, obligately lytic; for plasmid: incompatibility group; for eukaryote: asexual, sexual; other more specific values (e.g., incompatibility group) are allowed
Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage
for plasmid: antibiotic resistance; for phage: converting genes
Targeted gene or locus name for marker gene studies
Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA
PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters
Description of reaction conditions and components of polymerase chain reaction performed during library preparation.
initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles
Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA
Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences
The total number of tRNAs identified from the SAG or MAG
The approach used to determine the completeness of a given genomic assembly, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome
Amount of water vapour in the air, at the time of sampling
Methane (gas) amount or concentration at the time of sampling
micromole per liter, parts per billion, parts per million
Concentration of dissolved inorganic phosphorus in the sample
Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus
Measurement of bacterial carbon production
Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential
gram per gram or cubic centimeter per cubic centimeter
Porosity of deposited sediment is volume of voids divided by the total volume of sample
Ratio of amount or concentrations of carbon to nitrogen
Whether or not crop is rotated, and if yes, rotation schedule
Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes
Reference or method used in determining soil series name or other lower-level classification
Reference or method used in determining soil texture
Reference or method used in determining total organic carbon
Reference or method used in determining the total nitrogen
Measurement of mean peak friction velocity
Concentration of particulate organic carbon
Source of organic carbon in the culture rooting medium; e.g. sucrose
Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170 mg/L)
The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps
Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials smaller than the size threshold are excluded from the sample
Mesh or pore size of the device used to retain the sample. Materials larger than the size threshold are excluded from the sample.
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)
Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary
pH measurement of the culture rooting medium; e.g. 5.5
Reference or method used in determining pH
Text or terms that describe the geographic feature where the food sample was obtained by the researcher. This field accepts selected terms listed under the following ontologies: anthropogenic geographic feature (http://purl.obolibrary.org/obo/ENVO_00000002), for example agricultural fairground [ENVO:01000986]; garden [ENVO:00000011} or any of its subclasses; market [ENVO:01000987]; water well [ENVO:01000002]; or human construction (http://purl.obolibrary.org/obo/ENVO_00000070)
Number of bacteria in sample, as defined by bacteria density (http://purl.obolibrary.org/obo/GENEPIO_0000043)
A reference to a place on the Earth, by its name or by its geographical location that describes the origin of the food commodity, either in terms of its cultivation or production. This field accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448)
The maximum number of product units within a package
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)
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
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
Measurements of biologically distinct samples that show biological variation
Repeated measurements of the same sample that show independent measures of the noise associated with the equipment and the protocols
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
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
Container in which the sample was stored during transport. Indicate the location name
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
Temperature at which sample was transported, e.g. -20 or 4 degree Celsius
Sample incubation duration if unpublished or unvalidated method is used. Indicate the timepoint written in ISO 8601 format
Sample incubation temperature if unpublished or unvalidated method is used
For time-course research studies involving samples of the food commodity, indicate the total duration of the time-course study
Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) should also be provided (example: total prokaryotes; 3.5e7 cells per ml; qPCR)
organism name;measurement value;enumeration
A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups
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
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
A distinctive alpha-numeric identification code assigned by the manufacturer or distributor to a specific quantity of manufactured material or product within a batch. Synonym: Batch Number. The submitter should provide lot number of the item followed by the item name for which the lot number was provided
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
Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids)
The range and diversity of host species that an organism is capable of infecting, defined by NCBI taxonomy identifier
Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)
Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen
microgram per liter, micromole per liter, milligram per liter
Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2
milligram per cubic meter, microgram per liter
Measure of the amount of cloudiness or haziness in water caused by individual particles
Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)
Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types
Content of last meal and time since feeding; can include multiple values
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)
Any result of a bacterial culture experiment reported as a binary assessment such as positive/negative, active/inactive
Type of container or wrapping defined by the main container material, the container form, and the material of the liner lids or ends. Also type of container or wrapping by form; prefer description by material first, then by form. This field accepts terms listed under food container or wrapping (http://purl.obolibrary.org/obo/FOODON_03490100)
The reason that the sample was collected
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)
Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications. Indicate name of the sequencing kit
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
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."
A collection of metadata terms (slots) to minimally describe the sampling and sequencing method of a specimen used to generate a nucleotide sequence.
Relationships to other hosts in the same study; can include multiple relationships
A collection of terms appropriate when collecting and sequencing samples obtained from a gaseous environment.
bioaerosol samples, pathogen load in urban air, aerosols
A collection of terms appropriate when collecting samples and sequencing samples obtained in the built-up environment, which includes terms for surface material, humidity, temperature, moisture and occupancy type along with specific metadata terms describing the indoor air, building and sample properties.
microbiology studies of the built environment, NASA space station sampling, MetaSUB transit system sampling, home, hospitals, office buildings
A collection of terms appropriate when collecting samples and sequencing samples obtained from a non-human host, to examine the host-associated microbiome or genome.
This is a very broad package, intended to capture many kinds of sequences derived from the bodies of or derived from an organism. Where possible, please use a more specific package. For example, consider using food-animal and animal feed extension for sampling of farm animals reared for consumption. For human stool microbiomes, consider MIxS-human-gut. Incidental associations of environmental material with an organism may also be better served by other packages. For example, nucleic acids derived from soil that was sampled from the hoof of a cow may be better described by terms from the soil extension; however, soil embedded in a wound on a cow’s leg would be best described by terms in this extension
elephant fecal matter or cat oral cavity
A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their human-associated microbiome or genome, that does not have a specific extension (e.g., skin, gut, vaginal).
For stool samples use MIxS-human-gut extension.
A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their gut-associated microbiome.
human stool or fecal samples, or samples collected directly from the gut.
A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their oral-associated microbiome.
mouth swab sampling, dental microbiome samples, microbiome of oral swabs, nasal, mouth, throat, teeth, tongue microbiome studies
A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their skin-associated microbiome.
swab samples taken on a person’s skin surface.
A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their vaginal-associated microbiome.
A collection of terms appropriate when collecting samples and sequencing samples obtained from biofilm environments including microbial mats.
samples from microbial mats at cold seeps
miscellaneous natural or artificial environment
MIxS-miscellaneous natural or artificial environment
A collection of generic terms appropriate when collecting and sequencing samples obtained from environments, where there is no specific extension already available.
A collection of terms appropriate when collecting samples and sequencing samples obtained from a plant to examine its plant-associated microbiome.
plant surface swabs, root soil or rhizosphere, cultivated plants, plant phenotyping
A collection of terms appropriate when collecting samples and sequencing samples obtained from the sedimentary area of aquatic environments.
Sedimentary layers in terrestrial environments will probably be better served by the soil extension.
A collection of terms appropriate when collecting samples and sequencing samples obtained from the uppermost layer of Earth's crust, contributed by the Terragenome Consortium.
soil collection, island microbiome sampling, farm land or forest floor.
A collection of terms appropriate when collecting samples and sequencing samples obtained from any solid, semisolid or liquid waste.
A collection of terms appropriate when collecting samples and sequencing water samples obtained from any aquatic environment.
sea or river water, global ocean sampling day
A collection of terms appropriate when collecting samples and sequencing samples obtained from environments pertaining to hydrocarbon resources, specifically core samples.
The microbial characterization of hydrocarbon occurrences, defined as the natural and artificial environmental features that are rich in hydrocarbons, from hydrocarbon rich formations, such as reservoir cores.
MIxS-HCR (hydrocarbon resources-fluids/swabs)
A collection of terms appropriate when collecting samples and sequencing samples obtained from environments pertaining to hydrocarbon resources, specifically run-off liquids samples and swabs.
The microbial characterization of hydrocarbon occurrences, defined as the natural and artificial environmental features that are rich in hydrocarbons, from hydrocarbon resource fluids.
A collection of terms appropriate when sequencing samples obtained in an agricultural environment. Suitable to capture metadata appropriate to enhance crop productivity and agroecosystem health with the aim to facilitate research of agricultural microbiomes and their relationships to plant productivity and sustainable crop production from diverse crop management contexts.
Agricultural Microbiomes Research Coordination Network, model cropping and plant systems focused on agricultural plant and soil microbe; microbiome studies in agricultural sites; long-term ecological research in croplands; eDNA in manure samples; describing agricultural microbiome studies
A collection of terms appropriate when collecting samples and performing sequencing of samples obtained from farm animals and their feed.
This extension is intended to work alongside the other food extensions (farm environment, food production facility, and human foods) for capturing contextual data across the food supply-chain environment.
Microbiome of farm animals, their feed, and pet food.
A collection of terms appropriate when collecting samples and performing sequencing of samples obtained from the farm environment, including soil, manure, and food harvesting equipment.
This extension is intended to work alongside the other food extensions (animals and animal feed, food production facility, and human foods) for capturing contextual data across the food supply-chain environment.
Microbiome of farm and field crops as well as environmental samples including irrigation, soil amendments, and farm equipment.
A collection of terms appropriate when collecting samples and performing sequencing of samples obtained from food production facilities.
This extension is intended to work alongside the other food extensions (animals and animal feed, farm environment, and human foods) for capturing contextual data across the food supply-chain environment.
Microbiome of food production facilities/factories
A collection of terms appropriate when collecting samples and performing sequencing of samples obtained from human food products.
This extension is intended to work alongside the other food extensions (animals and animal feed, farm environment, and food production facilities) for capturing contextual data across the food supply-chain environment.
Microbiome of foods intended for human consumption.
A collection of terms appropriate when collecting samples and sequencing samples obtained from an organism that lives in close association with any other organism(s).
the microbiome sequence of a flea sampled from a farm animal
names of organisms that the entity is pathogenic to
Body mass index, calculated as weight/(height)squared
Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given
pooling status;number of pooled extracts
Resting pulse, measured as beats per minute
Concentration of magnesium in the sample
mole per liter, milligram per liter, parts per million, micromole per kilogram
Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid
micromole per liter, milligram per liter
Density of the sample, which is its mass per unit volume (aka volumetric mass density)
gram per cubic meter, gram per cubic centimeter
gram Carbon per kilogram sample material
Couldn't convert host_occupation with value veterinary to integer
almost all host_occupation values in the NCBI biosample_set are strings, not integers
Whether full medical history was collected
Type of plant or animal from which the food product or its major ingredient is derived or a chemical food source [FDA CFSAN 1995]
Packaged kits (containing adapters, indexes, enzymes, buffers etc.), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids
The location the sequencing run was performed. Indicate the name of the lab or core facility where samples were sequenced
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
The datetime marking the end of a process in which a sample yields a positive result for the target microbial analyte(s) in the form of an isolated colony or colonies
A food product type is a class of food products that is differentiated by its food composition (e.g., single- or multi-ingredient), processing and/or consumption characteristics. This does not include brand name products but it may include generic food dish categories. This field accepts terms under food product type (http://purl.obolibrary.org/obo/FOODON:03400361). For terms related to food product for an animal, consult food product for animal (http://purl.obolibrary.org/obo/FOODON_03309997). If the proper descriptor is not listed please use text to describe the food type. Multiple terms can be separated by one or more pipes
Filtering pore size used in sample preparation
The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period
Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object
Report the host's taxonomic name and/or NCBI taxonomy ID
Core body temperature of the host when sample was collected
Pressure to which the sample is subject to, in atmospheres
Concentration of potassium in the sample
milligram per liter, micromole per liter, parts per million
Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter
microgram per liter, milligram per liter, parts per million
Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample
example of non-binary from Excel sheets does not match any of the enumerated values
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
The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont can have its own symbionts. For example, parasites may have hyperparasites (=parasites of the parasite)
Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material
Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments
Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, 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
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters
Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate
milliequivalent per liter, milligram per liter
A unique identifier by which each subject can be referred to, de-identified
Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). Use terms from the foundational model of anatomy ontology (fma) or the Uber-anatomy ontology (UBERON)
Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. Use terms from the foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON)
A collection of recommended metadata terms (slots) developed by community experts, describing the specific context under which a sample was collected.
The phylogenetic marker(s) used to assign an organism name to the SAG or MAG
Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores
Tools used for completion estimate, i.e. checkm, anvi'o, busco
Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences
A related resource that is referenced, cited, or otherwise associated to the sequence
Minimal Information about a Genome Sequence: eukaryote
Minimal Information about a Genome Sequence: cultured bacteria/archaea
Minimal Information about a Genome Sequence: plasmid
Minimal Information about a Genome Sequence: virus
Minimal Information about a Genome Sequence: organelle
Minimal Information about a Marker Sequence: survey
for marker gene sequences obtained directly from the environment
Minimal Information about a Marker Sequence: specimen
for marker gene sequences from cultured or voucher-identifiable specimens
Minimum Information About a Single Amplified Genome
Minimum Information About a Metagenome-Assembled Genome
Minimum Information About an Uncultivated Virus Genome
Any changes made to MIMS should be reflected here, in MIMS-MISIP. This checklist includes all MIMS terms and additional MISIP terms.
pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid
A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2)
for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer
Variable aspects of an experiment design that can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI)
Primary publication if isolated before genome publication; otherwise, primary genome report
Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG
Method used to predict UViGs features such as ORFs, integration site, etc
List of database(s) used for ORF annotation, along with version number and reference to website or publication
names, versions, and references of databases
Tool used to compare ORFs with database, along with version and cutoffs used
Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes
Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees
Total mass of the host at collection, the unit depends on host
Phenotype of human or other host. Use terms from the phenotypic quality ontology (pato) or the Human Phenotype Ontology (HP)
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) (v 163), http://purl.bioontology.org/ontology/chebi
The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the large subunit (LSU) RNA, small subunit (SSU) and the presence of 5.8S rRNA or 5S rRNA depending on whether it is a eukaryotic or prokaryotic genome, respectively. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated
Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community
Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter
name of tool or pipeline used, or annotation source description
Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
Report the entity or entities which are in the sample or specimen s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
Environmental entities having causal influences upon the entity at time of sampling
Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top)
Total number of clones in the library prepared for the project
Total number of clones sequenced from the library
Specify whether to expect single, paired, or other configuration of reads
Cloning vector type(s) used in construction of libraries
Specific enrichment or screening methods applied before and/or after creating libraries
Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters
Tool(s) used for assembly, including version number and parameters
Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types
perturbation type name;perturbation interval and duration
NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome for mock community/positive controls, or 'blank sample' for negative controls
The substance or equipment used as a negative control in an investigation
The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive
A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed
List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text
A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids
Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)
Any other measurement performed or parameter collected, that is not listed here
Heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air
The method employed for collecting the sample
The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
geographic location (latitude and longitude)
The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees, limited to 8 decimal points, and in WGS84 system
geographic location (country and/or sea,region)
The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)
The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant
A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample
Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)
The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater
Location at which sample was stored, usually name of a specific freezer/room
Temperature at which sample was stored, e.g. -80 degree Celsius
Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format
The vertical distance below local surface. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples
Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit
Temperature of the sample at the time of sampling
Name of the project within which the sequencing was organized
sample volume or weight for DNA extraction
Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001)
milliliter, gram, milligram, square centimeter
A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name
A collection of Data that comply with some combination of a MIxS checklist and environmental extension
This file contains a YAML-formatted specification of the Minimum Information about any (x) Sequence (MIxS) standard, generated using LinkML (https://linkml.io/linkml/). This file is released by the Genomic Standards Consortium (GSC; https://www.gensc.org/) for use by anyone handling data or information about biological sequences. This file is also used as an authoritative 'source of truth' to generate downstream GSC artifacts, available here: https://github.com/GenomicsStandardsConsortium/mixs/tree/main/project
slot titles that are associated with more than one slot name/SCN: host sex