From bf5804f961e1669f46840001bb682434efa6c381 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 21 Mar 2024 09:53:30 -0400 Subject: [PATCH] add data assets and prepare for local/.env --- assets/extension_report.yaml | 163 +++ ...nvo_environmental_material_annotations.tsv | 1090 +++++++++++++++++ local/.gitkeep | 0 ...o_envo_envirnmental_materials_by_claude.py | 44 + poetry.lock | 321 ++++- pyproject.toml | 1 + 6 files changed, 1618 insertions(+), 1 deletion(-) create mode 100644 assets/extension_report.yaml create mode 100644 assets/report_envo_environmental_material_annotations.tsv create mode 100644 local/.gitkeep create mode 100644 nmdc_ontology/mixs_environments_extensions_to_envo_envirnmental_materials_by_claude.py diff --git a/assets/extension_report.yaml b/assets/extension_report.yaml new file mode 100644 index 0000000..f430055 --- /dev/null +++ b/assets/extension_report.yaml @@ -0,0 +1,163 @@ +Agriculture: + description: 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. + title: agriculture + use_cases: 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 +Air: + description: A collection of terms appropriate when collecting and sequencing obtained + from a gaseous environment. + title: air + use_cases: bioaerosol samples, pathogen load in urban air, aerosols +BuiltEnvironment: + description: 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. + title: built environment + use_cases: microbiology studies of the built environment, NASA space station sampling, + MetaSUB transit system sampling, home, hospitals, office buildings +FoodAnimalAndAnimalFeed: + comments: 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. + description: A collection of terms appropriate when collecting samples and performing + sequencing of samples obtained from farm animals and their feed. + title: food-animal and animal feed + use_cases: Microbiome of farm animals, their feed, and pet food. +FoodFarmEnvironment: + comments: 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. + description: 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. + title: food-farm environment + use_cases: Microbiome of farm and field crops as well as environmental samples including + irrigation, soil amendments, and farm equipment. +FoodFoodProductionFacility: + comments: 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. + description: A collection of terms appropriate when collecting samples and performing + sequencing of samples obtained from food production facilities. + title: food-food production facility + use_cases: Microbiome of food production facilities/factories +FoodHumanFoods: + comments: 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. + description: A collection of terms appropriate when collecting samples and performing + sequencing of samples obtained from human food products. + title: food-human foods + use_cases: Microbiome of foods intended for human consumption. +HostAssociated: + comments: 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 + description: 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. + title: host-associated + use_cases: elephant fecal matter or cat oral cavity +HumanAssociated: + comments: For stool samples use MIxS-human-gut extension. + description: 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). + title: human-associated + use_cases: blood samples or biopsy samples. +HumanGut: + description: A collection of terms appropriate when collecting samples and sequencing + samples obtained from a person to examine their oral-associated microbiome. + title: human-gut + use_cases: human stool or fecal samples, or samples collected directly from the + gut. +HumanOral: + description: A collection of terms appropriate when collecting samples and sequencing + samples obtained from a person to examine their oral-associated microbiome. + title: human-oral + use_cases: mouth swab sampling, dental microbiome samples, microbiome of oral swabs, + nasal, mouth, throat, teeth, tongue microbiome studies +HumanSkin: + description: A collection of terms appropriate when collecting samples and sequencing + samples obtained from a person to examine their skin-associated microbiome. + title: human-skin + use_cases: swab samples taken on a person's skin surface. +HumanVaginal: + description: A collection of terms appropriate when collecting samples and sequencing + samples obtained from a person to examine their vaginal-associated microbiome. + title: human-vaginal + use_cases: vaginal swabbing +HydrocarbonResourcesCores: + description: A collection of terms appropriate when collecting samples and sequencing + samples obtained from environments pertaining to hydrocarbon resources, specifically + core samples. + title: hydrocarbon resources-cores + use_cases: 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. +HydrocarbonResourcesFluidsSwabs: + description: 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. + title: hydrocarbon resources-fluids/swabs + use_cases: The microbial characterization of hydrocarbon occurrences, defined as + the natural and artificial environmental features that are rich in hydrocarbons, + from hydrocarbon resource fluids. +MicrobialMatBiofilm: + description: A collection of terms appropriate when collecting samples and sequencing + samples obtained from biofilm environments including microbial mats. + title: microbial mat/biofilm + use_cases: samples from microbial mats at cold seeps +MiscellaneousNaturalOrArtificialEnvironment: + description: A collection of generic terms appropriate when collecting and sequencing + samples obtained from environments, where there is no specific extension already + available. + title: miscellaneous natural or artificial environment +PlantAssociated: + description: A collection of terms appropriate when collecting samples and sequencing + samples obtained from a plant to examine it's plant-associated microbiome. + title: plant-associated + use_cases: plant surface swabs, root soil or rhizosphere, cultivated plants, plant + phenotyping +Sediment: + comments: Sedimentary layers in terrestrial environments will probably be better + served by the soil extension. + description: A collection of terms appropriate when collecting samples and sequencing + samples obtained from the sedimentary area of aquatic environments. + title: sediment + use_cases: river bed or sea floor. +Soil: + description: 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. + title: soil + use_cases: soil collection, island microbiome sampling, farm land or forest floor. +SymbiontAssociated: + description: 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). + title: symbiont-associated + use_cases: the microbiome sequence of a flea sampled from a farm animal +WastewaterSludge: + description: A collection of terms appropriate when collecting samples and sequencing + samples obtained from any solid, semisolid or liquid waste. + title: wastewater/sludge + use_cases: sewerage or industrial wastewater +Water: + description: A collection of terms appropriate when collecting samples and sequencing + water samples obtained from any aquatic environment. + title: water + use_cases: sea or river water, global ocean sampling day diff --git a/assets/report_envo_environmental_material_annotations.tsv b/assets/report_envo_environmental_material_annotations.tsv new file mode 100644 index 0000000..fb097ab --- /dev/null +++ b/assets/report_envo_environmental_material_annotations.tsv @@ -0,0 +1,1090 @@ + IAO_0000115 hasExactSynonym comment label IAO_0000116 hasBroadSynonym hasNarrowSynonym hasRelatedSynonym +ENVO_00010483 ['A material entity which other material entities in an environmental system are primarily or partially composed of.'] ['portion of environmental material'] "['Everything under this parent must be a mass noun (i.e. not countable). All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, ""ENVO:water"" is to be understood as ""environmental material composed primarly of some CHEBI:water"".', 'Instances of this class are portions of environmental materials, such as seawater in bucket, a water parcel in the photic zone of a lake, or the concrete that composes a building part. Instances of these portions may have fiat or non-fiat boundaries. For example, a water parcel has not physical boundaries, while the seawater in a bucket is bounded by the internal surfaces of the bucket.']" ['environmental material'] +ENVO_0010001 ['Anthropogenic material in or on which organisms may live.'] ['anthropogenic environmental material'] +ENVO_01000406 ['Snow is an environmental material which is primarily composed of flakes of crystalline water ice.'] ['snow'] +ENVO_00000134 ['An environmental material which is 1) composed primarily of soil or rock and included ice or organic material and 2) at or below the freezing point of water for two or more years.'] ['Ice is not always present, as may be in the case of nonporous bedrock, but it frequently occurs and it may be in amounts exceeding the potential hydraulic saturation of the ground material.'] ['permafrost'] +ENVO_00001998 ['An environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, interstitial gases, liquids, and a broad range of resident micro- and macroorganisms.'] "['\'In engineering terms, soil is referred to as regolith, or loose rock material that lies above the \'solid geology\'. Soil is commonly referred to as ""earth"" or ""dirt""; technically, the term ""dirt"" should be restricted to displaced soil.\' https://en.wikipedia.org/wiki/Soil\n\n"" The upper limit of soil is the boundary between soil and air, shallow water, live plants, or plant materials that have not begun to decompose. Areas are not considered to have soil if the surface is permanently covered by water too deep (typically more than 2.5 meters) for the growth of rooted plants.\n\nThe lower boundary that separates soil from the nonsoil underneath is most difficult to define. Soil consists of horizons near the Earth\'s surface that, in contrast to the underlying parent material, have been altered by the interactions of climate, relief, and living organisms over time. Commonly, soil grades at its lower boundary to hard rock or to earthy materials virtually devoid of animals, roots, or other marks of biological activity. For purposes of classification, the lower boundary of soil is arbitrarily set at 200 cm."" Soil taxonomy, 2nd Ed., quoted in http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280']" ['soil'] "[""The various 'has part' and 'has quality' relations may not hold true for all soils; however, I have yet to find counter examples. Require input from a pedologist or similar. [pbuttigieg]""]" ['regolith'] +ENVO_01000814 ['An environmental material which is in a solid state.'] ['This is a defined class: its subclasses will not be asserted, but filled by inference.'] ['solid environmental material'] +ENVO_01000001 ['An environmental material which is a liquid or semi-liquid mixture of water and some combination of soil, silt, and clay particles.'] ['mud'] +ENVO_01000155 ['Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.'] ['biomass'] ['organic material'] +ENVO_00002264 ['A material which is not the desired output of a process and which is typically the input of a process which removes it from its producer (e.g. a disposal process).'] ['waste material'] "['This seems more like a role than a material. Anything can be waste. Thus, a ""waste"" role or disposition will be created and this class can then be populated by inference: any environmental material which has [role,disposition] waste will be considered a waste material.']" +ENVO_01000060 ['An environmental material which is composed primarily of particles.'] ['particulate environmental material'] ['Do not oversimplify this branch with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.'] ['particulate matter'] +ENVO_03501300 ['An environmental material consisting of organic matter from plants and/or animals that is used in agriculture as fertilizer.'] ['Most manure consists of animal feces; other sources include compost and green manure.'] ['manure'] ['animal manure', 'compost', 'farm slurry', 'green manure', 'liquid manure'] +ENVO_00002191 "[""Straw or other material strewn in an animal's enclosure (e.g. a stable) for it to sleep on and to absorb its faeces and urine.""]" ['animal litter'] +ENVO_00003930 ['A layer of impurities that accumulates at the surface of a liquid (especially water or molten metal).'] ['scum'] +ENVO_00005738 ['An environmental material which has the quality of a foam.'] ['foamy environmental material'] +ENVO_00010505 ['Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets.'] "['Should connect to PATO as ""quality of an aerosol""']" ['aerosol'] +ENVO_00010506 ['A mixture of two immiscible (unblendable) substances. One substance (the dispersed phase) is dispersed in the other (the continuous phase).'] ['emulsion'] +ENVO_02000140 ['An environmental material which is unable to resist shear forces and continuously deforms when subject to them.'] ['fluid environmental material'] ['fluid'] +ENVO_01000637 ['Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies.'] ['outer space'] ['space'] +ENVO_01000575 ['A wax is an environmental material which is primarily composed of lipids or other organic compounds that consist of long alkyl chains. Waxes are are malleable near ambient temperatures and melt at approximately 45 degrees Celsius.'] ['wax'] +ENVO_01000939 ['An open system in non-equilibrium with its environment that exhibits time translation symmetry breaking.'] ['space-time crystal'] ['While the usage of the term is still debated, the general idea is that time crystals (which have been made using ytterbium ions and defect-bearing diamonds) break temporal symmetry analogously to how mineral crystal break spatial symmetry. While spatial crystals are inhomogeneous in space (vs a gas, which is distributed evenly) due to the ordering of their atoms, the properties of atoms in a time crystal are inhomogeneous in the time dimension.'] ['time crystal'] +ENVO_01001069 ['A material which is composed primarily of one or more pure metals and which shows their properties.'] ['While this class allows for some degree of contamination by non-metal substances, the material represented should show at least some of the typical features of a pure metal: hardness (except for liquid metals), opacity, lustre, malleability, fusibility, ductile and good electrical and thermal conductivity.'] ['metallic material'] ['Far more axiomatisation can be done should the qualities of metals be added to PATO or a similar quality ontology. However, note that there are many exceptions to the typical qualities of the majority of metals.'] ['metal'] +ENVO_01001154 ['A material which is composed primarily of chemical elements and compounds with relatively low boiling points, equilibrium condensation temperatures below 1300 Kelvin, and which are part of the crust or atmosphere of a moon or planet.'] ['Examples include nitrogen, water, carbon dioxide, ammonia, hydrogen, methane and sulfur dioxide. In astrogeology, these compounds, in their solid state, often comprise large proportions of the crusts of moons and dwarf planets.'] ['volatile astrogeological material'] ['Add and axiomatise with moon and lunar crust'] ['volatile'] +ENVO_01001156 ['A material which is composed primarily of chemical elements and compounds which have equilibrium condensation temperatures above approximately 1300 Kelvin and which are part of the crust or atmosphere of a moon or planet.'] ['The refractory group includes elements and compounds like metals and silicates (commonly termed rocks) which make up the bulk of the mass of the terrestrial planets and asteroids in the inner belt.'] ['refractory astrogeological material'] ['Add and axiomatise with moon and lunar crust'] ['refractory material'] +ENVO_01001202 ['Soil or sediment which has been eroded and influenced by flowing water and redeposited in a non-marine setting.'] ['alluvium'] +ENVO_01001560 ['An environmental material which is primarily composed of a dispersed phase of insoluable particles, approximately between 1 nanometer and 1 micrometer in maximum dimension, distributed throughout a material acting as a medium of suspension.'] ['Wikipedia lists several forms of colloidal suspension such as colloidal aerosols, colloidal emulsions, colloidal foams, colloidal dispersions, or hydrosols.'] ['colloidal suspension'] ['colloid'] +ENVO_01001649 ['An environmental material which is denser than bromoform.'] ['heavy fraction material'] ['Axiomatising this with relational density qualities pinned to bromoform would be the next step.'] +ENVO_01001650 ['An environmental material which is less dense than bromoform.'] ['light fraction material'] ['Axiomatising this with relational density qualities pinned to bromoform would be the next step.'] +ENVO_02000004 ['Nesting material is an animal habitation consisting of matierals used to cushion, insulate and protect the young of the organism. The adult will use the material to form a protective structure to house and raise their young. Nests are built primarily by birds, but also by mammals, fish, insects and reptiles.'] ['nesting material'] +FOODON_00002403 ['Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience'] ['food', 'foodstuff', 'nourishment', 'sustenance'] "[""This class is the top of FOODON's main food product hierarchy which is described in the https://www.foodon.org website, and can be searched in lookup services like https://www.ebi.ac.uk/ols/""]" ['food material'] +ENVO_03000076 ['A slurry of frazil, snow, and liquid water.'] ['These new ice classes refer to both marine water and fresh water ice. If using this term for annotation, use it in conjunction with another envo term to express whether the ice is in a marine, freshwater, or other system.'] ['slush ice'] +ENVO_03501259 ['Environmental material consisting of waste products that have been discarded at an unsuitable location.'] ['litter'] +ENVO_03501303 ['Macromolecules that are obtained naturally from plants or animals.'] ['natural-based polymer'] +ENVO_03501306 ['A polyester film made from stretched polyethylene terephthalate (PET).'] ['BoPET (Biaxially-oriented polyethylene terephthalate)'] ['mylar'] +ENVO_03510015 ['A polysaccharide that functions as an emulsifier, stabilizer, and thickener in mixtures.'] ['xanthan gum'] +ENVO_03510016 ['A naturally occurring plant-based gum, which functions as a viscous, odorless, tasteless, water-soluble mixture of polysaccharides that absorbs water to become a gel/paste.'] ['shiraz gum', 'tragacanth gum'] ['Tragacanth has many uses, including as an emulsifier, thickener, stabilizer, and texturant additive for foods, pharmaceuticals, and art materials.'] ['tragacanth'] +ENVO_03510018 ['A solid or highly viscous plant or synthetic based substance that is typically convertible into polymers.'] ['resin'] +ENVO_03510023 ['A resin secreted by the female lac bug, which is dissolved in alcohol to be used as a brush-on colorant, food glaze, and wood finish.'] ['shellack'] ['shellac'] +ENVO_03510037 ['Any material containing unstable atoms that emit ionizing radiation as it decays.'] ['radioactive material'] +ENVO_03510038 ['An environmental material which is primarily composed of cyanoacrolate.'] ['Cyanoacrylates have industrial, medical, and household uses. A strong fast-acting adhesive which is an ester of cyanoacrylic acid.'] ['volume of cyanoacrylate'] +ENVO_03510064 ['An environmental material which is composed primarily of gases and particles produced by the combustion of petroleum fuels.'] ['emissions from petroleum combustion'] +ENVO_03600013 ['An environmental material which consists of either loose sands or partially consolidated sandstone, containing a naturally occurring mixture of sand, clay, and water, soaked with a dense and extremely viscous form of petroleum.'] ['crude bitumen', 'oil sands', 'tar sands'] ['bituminous sand'] "['TODO: create an astonomical body part \'bituminous sands"" and assert composed primarily of realtionship. Xref https://github.com/EnvironmentOntology/envo/issues/1154.\n\nTREATED THIS as a material entity. could add something like ""oil sands deposit"" as a geospatial location later.']" +ENVO_03600017 ['An environmental material which is composed of insoluble solid particles suspended in a liquid.'] ['slurry'] "[""term requester also included and , but they may only be found in wikipedia's definition""]" +ENVO_06105003 ['An environmental material which is capable of, repeatedly, becoming plastic when heated and hardening again when cooled.'] ['thermoplastic material'] +ENVO_06105101 ['An environnmental material which 1) is composed primarily of polymers with high molecular mass and 2) once deformed does not spontaneously return to its original shape.'] ['Plastik', 'plastica', '塑膠'] "['""High molecular mass"" can be ambiguous as it does not set a threshold for what is considered ""high"". Here we make no commitment to a threshold.']" ['plastic'] ['Kunststoff'] +ENVO_00000003 ['Mine tailings are the materials left over after the process of separating the valuable fraction from the uneconomic fraction (gangue) of an ore.'] ['mine tailing'] ['tailing'] +ENVO_00002044 ['The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes.'] ['sludge'] +ENVO_00002230 ['Anthrosols comprise soils that have been modified profoundly through human activities, such as addition of organic materials or household wastes, irrigation and cultivation.'] ['anthrosol'] +ENVO_00002870 ['A natural building material mode from sand, clay, water, and some kind of fibrous or organic material (sticks, straw, and/or manure).'] ['adobe'] +ENVO_01000458 ['Concrete is a composite material composed of an aggregate bonded together with a fluid cement which hardens over time.'] "['Missing the class for ""aggregate"" - tricky to define what it is, exactly. Again, seems more like some sort of material/disposition hybrid.']" ['concrete'] +ENVO_01000462 ['Masonry cement is a substance used in construction that has the disposition to set and harden and thus may be used to bind materials together.'] "['""Cement"" refers more to a disposition than a specific material.']" ['masonry cement'] ['cement'] +ENVO_01000461 ['Refined asphalt is a sticky, black, and highly viscous liquid or semi-solid with a boiling point above 500 degrees Celsius, obtained from the fractional distillation of crude oil.'] ['refined bitumen'] ['refined asphalt'] +ENVO_01000474 ['A portion of brick material is a material derived from a brick which is composed of kneaded clay-bearing soil, expanded clay aggregate, sand and lime, or concrete that has been fire-hardened or air-dried.'] ['brick material'] +ENVO_01000476 ['Plaster is a building material which has the disposition to harden when it reacts with water, liberating heat through crystallization. Plaster is manufactured as a dry powder and is mixed with water to form a paste when used.'] ['stucco', 'render'] ['plaster'] +ENVO_01001869 ['A liquid environmental material which is composed primarily of water ammended with thickening agents and proppants.'] ['fracking liquid'] ['fracking water'] +ENVO_02000123 ['Any liquid, liquefiable, or mastic composition that, after application to a substrate in a thin layer, converts to a solid film. It is most commonly used to protect, color, or provide texture to objects.'] ['paint'] +ENVO_03501253 ['A soft sulfate mineral composed of calcium sulfate dihydrate.'] ['gypsum'] +ENVO_03501324 ['A stable dispersion (emulsion) of polymer microparticles in an aqueous medium.'] ['Natural rubber, India rubber, Gum elastic, Non-vulcanized rubber'] ['Latex is made by some plants, but synthetic latexes can be manufactured as well.'] ['latex'] +ENVO_03510055 ['An environmental material which is composed of elastic polymers mixed in a solvent.'] ['cow gum'] ['Solvents typically used include acetone, hexane, heptane or toluene.'] ['rubber cement'] +ENVO_03510056 ['An environmental material which is 1) composed primarily of methyl cellulose and water, and 2) formulated to fix wallpaper to walls.'] ['wallpaper adhesive', 'wallpaper paste'] ['methyl cellulose paste'] +ENVO_03510057 ['An environmental material which is 1) manufactured and 2) primarily composed of hydrogen peroxide and ammonia, and 3) when applied to hair, can alter the natural hair pigments for 6-8 weeks.'] ['permanent hair dye'] ['hair color'] +ENVO_03510058 ['A colorant fluid which is 1) manufactured and 2) composed of alcohol, titanium dioxide, and propylene glycol.'] ['pharmaceutical ink'] +ENVO_03510060 ['A colorant fluid which is 1) manufactured and 2) composed of copper phthalocyanine, iron oxides, water, and biopolymers.'] ['gel ink'] +ENVO_03510061 ['A colorant fluid which is 1) manufactured and 2) primarily composed of soybean oil, as well as pigment, resin, and wax.'] ['soy ink'] +ENVO_03510062 ['A colorant fluid which is 1) manufactured, 2) primarily composed of water, as well as glycol, and dye, and 3) intended for use in inkjet printers.'] ['aqueous inkjet printer ink'] +ENVO_01001876 ['Snow which is composed of heavily rimed particles typically 2 to 5 millimeters in diameter (0.1 to 0.2 inch).'] ['Often indistinguishable from very small soft hail except for the size convention that hail must have a diameter greater than 5 mm. Sometimes distinguished by shape into conical, hexagonal, and lump (irregular) graupel.'] ['graupel'] ['Subclass by shape into conical, hexagonal, and lump (irregular) graupel. Mark Parsons notes that the formational processes may be a source of useful differentia to distinguish graupel from other snow types.'] ['snow pellets'] +ENVO_03000000 ['Partially compacted granular snow, which has undergone several cycles of melting and refreezing while being compacted, usually found on the atmosphere-exposed surface of a glacier.'] ['névé'] ['Névé that survives a full season of ablation turns into firn.'] ['neve'] +ENVO_03000027 ['Uncompacted snow containing trapped atmospheric gases.'] ['Described as having a fluffy appearance.'] ['powdery snow'] +ENVO_03000002 ['Granular snow which contains a proportion of fused granules formed through melting and re-thawing while being compacted by the weight of overlying material and which contains interconnected gaseous pores.'] ['Firn derives from névé which has survived a full season of ablation and has undergone a metamorphic transition.'] ['firn'] +ENVO_03000108 ['Snow which is cohesive, hard and overlies weaker snow.'] ['slab snow'] +ENVO_01001614 ['Permafrost which contains inclusions of water-based ice.'] ['ice-bearing permafrost'] +ENVO_03000088 ['Permafrost which contains pockets of trapped methane gas.'] ['bulgunyakh'] ['Other hydrocarbon gasses such as carbon dioxide may also be present. These pockets can be sufficently large that the permafrost surface will undulate when pressure is applied.'] ['methane-laden permafrost'] ['It would probably be better to assert parthood between the permafrost and cavities filled with gas rather than the gases themselves.'] +ENVO_00002871 ['Soil which has been eroded and influenced by flowing water and redeposited in a non-marine setting.'] ['alluvial soil'] +ENVO_00003082 ['A portion of enriched soil is a portion of soil with elevated levels of some material entity.'] ['This could be demoted to an inferred class if issues with double inheritance arise.'] ['enriched soil'] +ENVO_00002229 ['Arenosols are sandy soils, including both soils developed in residual sands after in situ weathering of usually quartz-rich sediments or rock, and soils developed in recently deposited sands such as dunes in deserts and beach lands.'] ['psamment', 'sandy soil'] ['arenosol'] +ENVO_00002231 ['Alisols are soils that have a higher clay content in the subsoil than in the topsoil as a result of pedogenetic processes (especially clay migration) leading to an argic subsoil horizon. Alisols have a low base saturation at certain depths and high-activity clays throughout the argic horizon. They lack the albeluvic tonguing as in Albeluvisols. They occur predominantly in humid tropical, humid subtropical and warm temperate regions.'] ['alisol'] +ENVO_00002232 ['Andosols are soils that develop in volcanic ejecta or glasses under almost any climate (except under hyperarid climate conditions). However, Andosols may also develop in other silicate-rich materials under acid weathering in humid and perhumid climates.'] ['andosol'] +ENVO_00002233 ['Albeluvisols are soils that have, beginning within 1 m of the soil surface, a clay illuviation horizon with an irregular or broken upper boundary resulting in tonguing of bleached soil material into the illuviation horizon.'] ['albeluvisol'] +ENVO_01001397 ['A soil which has high mineral content and which contain no calcareous material, have less than 10% weatherable minerals its surface layer, and have less than 35% base saturation throughout its volume.'] ['red clay soil'] "['The word ""ultisol"" is derived from ""ultimate"", because ultisols were seen as the ultimate product of continuous weathering of minerals in a humid, temperate climate without new soil formation via glaciation.']" ['ultisol'] +ENVO_00002235 ['Cambisols combine soils with at least an incipient subsurface soil formation. Transformation of parent material is evident from structure formation and mostly brownish discoloration, increasing clay percentage, and/or carbonate removal.'] ['cambisol'] +ENVO_01001526 ['Soil which is below the freezing point of water.'] ['frozen soil'] +ENVO_00002237 ['Chernozems are soils with a thick black surface layer that is rich in organic matter.'] ['chernozem'] ['black earth', 'boroll'] +ENVO_00002238 ['Durisols are associated mainly with old surfaces in arid and semi-arid environments and accommodate very shallow to moderately deep, moderately well- to well-drained soils that contain cemented secondary silica (SiO2) within 100 cm of the soil surface.'] ['durisol'] +ENVO_00002239 ['Calcisols are soils in which there is substantial secondary accumulation of lime. Calcisols are common in highly calcareous parent materials and widespread in arid and semi-arid environments.'] ['calcarosol'] ['calcisol'] +ENVO_00002240 ['Kastanozems are dry grassland soils, among them the zonal soils of the short-grass steppe belt, south of the Eurasian tall-grass steppe belt with Chernozems. Kastanozems have a similar profile to that of Chernozems but the humus-rich surface horizon is thinner and not as dark as that of the Chernozems and they show more prominent accumulation of secondary carbonates.'] ['kastanozem'] +ENVO_00002241 ['Leptosols are very shallow soils over continuous rock and soils that are extremely gravelly and/or stony. Leptosols are azonal soils and particularly common in mountainous regions.'] ['leptosol'] ['gravelly soil', 'stony soil'] +ENVO_00002242 ['Lixisols are soils that have a higher clay content in the subsoil than in the topsoil as a result of pedogenetic processes (especially clay migration) leading to an argic subsoil horizon. Lixisols have a high base saturation and low-activity clays at certain depths.'] ['lixisol'] +ENVO_00002243 ['Histosols comprise soils formed in organic material. These vary from soils developed in predominantly moss peat in boreal, arctic and subarctic regions, via moss peat, reeds/ sedge peat (fen) and forest peat in temperate regions to mangrove peat and swamp forest peat in the humid tropics. Histosols are found at all altitudes, but the vast majority occurs in lowlands.'] ['histosol'] +ENVO_00002244 ['Gleysols are wetland soils that, unless drained, are saturated with groundwater for long enough periods to develop a characteristic gleyic colour pattern. This pattern is essentially made up of reddish, brownish or yellowish colours at ped surfaces and/or in the upper soil layer or layers, in combination with greyish/bluish colours inside the peds and/or deeper in the soil.'] ['gleysol'] ['gley soil'] +ENVO_00002245 ['Gypsisols are soils with substantial secondary accumulation of gypsum (calcium sulfate). These soils are found in the driest parts of the arid climate zone.'] ['gypsisol'] +ENVO_00002246 ['Ferralsols represent the classical, deeply weathered, red or yellow soils of the humid tropics. These soils have diffuse horizon boundaries, a clay assemblage dominated by low-activity clays (mainly kaolinite) and a high content of sesquioxides.'] ['ferralsol'] ['oxisol'] +ENVO_00002247 ['Nitisols are deep, well-drained, red, tropical soils with diffuse horizon boundaries and a subsurface horizon with more than 30 percent clay and moderate to strong angular blocky structure elements that easily fall apart into characteristic shiny, polyhedric (nutty) elements. Weathering is relatively advanced but Nitisols are far more productive than most other red, tropical soils.'] ['nitisol'] +ENVO_00002248 ['Luvisols are soils that have a higher clay content in the subsoil than in the topsoil as a result of pedogenetic processes (especially clay migration) leading to an argic subsoil horizon. Luvisols have high-activity clays throughout the argic horizon and a high base saturation at certain depths.'] ['luvisol'] +ENVO_00002249 ['Phaeozems accommodate soils of relatively wet grassland and forest regions in moderately continental climates. Phaeozems are much like Chernozems and Kastanozems but are leached more intensively. Consequently, they have dark, humus rich surface horizons that, in comparison with Chernozems and Kastanozems, are less rich in bases. Phaeozems may or may not have secondary carbonates but have a high base saturation in the upper metre of the soil.'] ['phaeozem'] +ENVO_00002250 ['Plinthosols are soils with plinthite, petroplinthite or pisoliths. Plinthite is an Fe-rich (in some cases also Mn-rich), humus-poor mixture of kaolinitic clay (and other products of strong weathering such as gibbsite) with quartz and other constituents that changes irreversibly to a layer with hard nodules, a hardpan or irregular aggregates on exposure to repeated wetting and drying. Petroplinthite is a continuous, fractured or broken sheet of connected, strongly cemented to indurated nodules or mottles. Pisoliths are discrete strongly cemented to indurated nodules. Both petroplinthite and pisoliths develop from plinthite by hardening.'] ['plinthosol'] +ENVO_00002251 ['Planosols are soils with a light-coloured, surface horizon that shows signs of periodic water stagnation and abruptly overlies a dense, slowly permeable subsoil with significantly more clay than the surface horizon.'] ['planosol'] +ENVO_00002252 ['Solonchaks are soils that have a high concentration of soluble salts at some time in the year. Solonchaks are largely confined to the arid and semi-arid climate zones and to coastal regions in all climates.'] ['solonchak'] +ENVO_00002253 ['Umbrisols are soils in which organic matter has accumulated within the mineral surface soil (in most cases with low base saturation) to the extent that it significantly affects the behaviour and utilization of the soil.'] ['umbrisol'] +ENVO_00002254 ['A soil in which there is a high content of expansive clay known as montmorillonite that forms deep cracks in drier seasons or years. Alternate shrinking and swelling causes self-mulching, where the soil material consistently mixes itself, causing vertisols to have an extremely deep A horizon and no B horizon.'] ['vertisol'] +ENVO_00002255 ['Solonetz are soils with a dense, strongly structured, clayey subsurface horizon that has a high proportion of adsorbed Na and/or Mg ions. Solonetz that contain free soda (Na2CO3) are strongly alkaline (field pH > 8.5).'] ['solonetz'] +ENVO_00002256 ['Regosols form a taxonomic remnant group containing all soils that could not be accommodated in any of the other RSGs. In practice, Regosols are very weakly developed mineral soils in unconsolidated materials that do not have a mollic or umbric horizon, are not very shallow or very rich in gravels (Leptosols), sandy (Arenosols) or with fluvic materials (Fluvisols). Regosols are extensive in eroding lands, particularly in arid and semi-arid areas and in mountainous terrain.'] ['regosol'] +ENVO_00002257 ['Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics.'] ['podsol'] ['podzol'] ['podosolic soil'] +ENVO_00002258 ['A soil which is composed of approximately equal proportions of sand and silt, with a smaller proportion of clay.'] ['Some authorities consider loam to be any soil material that contains 7 to 27% clay, 28 to 50% silt, and less than 52% sand.'] ['loam'] +ENVO_00002259 ['Soil which is part of an ecosystem used for agricultural activities.'] ['agricultural soil'] +ENVO_00005786 ['Soil which is part of some elevated land.'] ['upland soil'] +ENVO_00002261 ['A portion of soil which is found in a forested area.'] ['forest soil'] +ENVO_00002262 ['Soil which is primarily composed of clay.'] ['clay soil'] +ENVO_00002263 ['A portion of soil which is found in a garden.'] ['garden soil'] +ENVO_00002273 ['Fluvisols accommodate genetically young, azonal soils in alluvial deposits.'] ['fluvisol'] +ENVO_00002274 ['Stagnosols are soils with a perched water table showing redoximorphic features caused by surface water. Stagnosols are periodically wet and mottled in the topsoil and subsoil, with or without concretions and/or bleaching.'] ['stagnosol'] +ENVO_00002275 ['Technosols are soils whose properties and pedogenesis are dominated by their technical origin. They contain a significant amount of artefacts (something in the soil recognizably made or extracted from the earth by humans), or are sealed by technic hard rock (material created by humans, having properties unlike natural rock). They include soils from wastes (landfills, sludge, cinders, mine spoils and ashes), pavements with their underlying unconsolidated materials, soils with geomembranes and constructed soils in human-made materials.'] ['technosol'] +ENVO_00005755 ['Soil which is part of an agricultural field.'] ['field soil'] +ENVO_00005741 ['Soil which is part of an alpine environment.'] ['alpine soil'] +ENVO_00005742 ['Soil which is capable of supporting the growth of crops.'] ['arable soil'] +ENVO_00005743 ['A portion of soil which is found in a roadside area.'] ['roadside soil'] +ENVO_00005750 ['A portion of soil which is found in a grassland.'] ['grassland soil'] +ENVO_00005747 ['Soil which is derived from compost.'] ['compost soil'] +ENVO_00005748 ['Soil which has little to no water content and in which minerals and other soluble chemical entities have either bonded or become adsorbed to sold particles due to insufficient water availability.'] ['dry soil'] +ENVO_00005749 ['A portion of soil which is part of a cropland or a rangeland biome.'] ['farm soil'] +ENVO_00005751 ['Soil which is part of a densely forested area subject to tropical climate patterns.'] ['jungle soil'] +ENVO_00005752 ['Soil which is part of a sawah, a wet or irrigated rice field.'] ['sawah soil'] +ENVO_00005754 ['Soil which has been amended with fertilizers.'] ['fertilized soil'] +ENVO_00005756 ['Soil which is formulated to promote the growth of grasses or other plants used to establish managed areas of vegetation.'] ['lawn soil'] +ENVO_00005760 ['Soil which has been transformed through a combustion process.'] ['burned soil'] ['burnt soil'] +ENVO_00005761 ['Soil which is part of a meadow.'] ['meadow soil'] +ENVO_00005764 ['Soil which is adjacent to a pond.'] ['pond soil'] +ENVO_00005766 ['Soil which has been amended with mineral additives to increase its pH.'] ['Common liming agents include calcium- and magnesium-rich materials in various forms, including marl, chalk, limestone, burnt lime or hydrated lime. Liming often improves plant growth and increases the activity of soil bacteria, but oversupply may result in harm to plant life.\nLiming can also improve aggregate stability on clay soils. For this purpose structure lime, products containing calcium oxide (CaO) or hydroxide (Ca(OH)2) in mixes with calcium carbonate (CaCO3), are often used. Structure liming can reduce losses of clay and nutrients from soil aggregates.'] ['limed soil'] +ENVO_00005767 ['Soil which has, as a part, a portion of either fresh or processed animal manure.'] ['manured soil'] +ENVO_00005768 ['Soil which has properties to which plants in the Family Orchidaceae have adapted, including increased levels of aeration and drainage.'] ['orchid soil'] +ENVO_00005771 ['Soil which is composed of a large proportion of mud, thus having properties resembling mud.'] ['muddy soil'] +ENVO_00005773 ['Soil which is found in a pasture and in which vegetation, such as the grass used for the grazing of ungulates, grows.'] ['pasture soil'] +ENVO_00005778 ['Soil which is part of a tropical environment.'] ['tropical soil'] +ENVO_00005780 ['A portion of soil which is found in a greenhouse.'] ['greenhouse soil'] +ENVO_00005781 ['Soil which is has been heated such that its chemical, physical, or biological properties are destabilised.'] ['heat stressed soil'] +ENVO_00005782 ['Soil which is formed from avian fecal matter.'] ['ornithogenic soil'] +ENVO_00005790 ['Soil which has 1) low concentrations of nutrients and humus, 2) low water retention capacity, 3) textural variation from sand to clay, 4) a porous and friable structure, and 5) low concentrations of soluble salts.'] ['Red soil typically derives from crystalline rock in warm, temperate, moist climates under deciduous or mixed forest. It has thin organic and organic-mineral layers, a black brown leached layer resting on an illuvium red layer. The majority of red soils have a loamy texture. Their chemical composition varies across regions, but often includes non-soluble material 90.47%, iron 3.61%, aluminium 2.92%, organic matter 1.01%, magnesium 0.70%, lime 0.56%, carbon dioxide 0.30%, potash 0.24%, soda 0.12%, phosphorus 0.09% and nitrogen 0.08%. \n\nOn the uplands, they are thin, poor and gravelly, sandy, or stony and porous, light-colored soils on which food crops like bajra can be grown. In contrast, on the lower plains and valleys they are rich, deep, dark colored fertile loam on which, under irrigation, can produce excellent crops like cotton, wheat, pulses, tobacco, jowar, linseed, millet, potatoes and fruits.'] ['red soil'] +ENVO_00005802 ['Soil that is not penetrated by the root systems of plants.'] ['bulk soil'] +ENVO_01001185 ['Soil which has increased levels of molecules or ions capable of donating a hydron (proton or hydrogen ion) to other chemical entities, or, alternatively, capable of forming covalent bonds with other chemicals via the acceptance of an electron pair, resulting in a bulk pH measurement of less than 7.'] ['acidic soil'] +ENVO_01001616 ['Soil which is directly exposed to the atmosphere - with no intervening layer of plant life or other cover - and thus the effects of weathering and erosion.'] ['bare soil'] +ENVO_01001638 ['Soil in which segregated ice will form (causing frost heave) under the required conditions of moisture supply and temperature.'] ['frost-susceptible soil'] ['The label would apply to all soils in which frost can form, however, the definition of this class suggests that ice segregation is a key property that differentiates this type of soil from others.'] +ENVO_02000059 ['A soil consisting of the upper layer of soil on the surface consisting of loose material capable of supporting life composed of a mixture of mineral and organic matter.'] ['topsoil'] ['surface soil'] +ENVO_02000138 ['Soil which is located in a mangrove biome.'] ['mangrove soil'] ['Mangrove soils are typically saline, anoxic, acidic and frequently waterlogged.'] ['mangrove biome soil'] +ENVO_06105205 ['A soil which has a high bulk density and/or a low porosity. A compacted soil has a reduced rate of both water infiltration and drainage'] ['compacted soil'] +ENVO_03600036 "[""Soil which has properties that restrict a pathogen's ability to establish itself, persist, or cause disease that results in long-term harm.""]" ['disease-suppressive soil'] ['The pathogenicity that is suppressed is typically directed towards plants, especially crops. Soils are typically classified as pathogen-suppressive if a pathogen 1) cannot establish itself or persist, 2) is able to establish itself, but causes little or no damage, or 3) is able to establishe itself, but only causes disease that does not result in long-term harm.'] ['pathogen-suppressive soil'] +ENVO_01000018 ['An environmental material which is composed primarily of pieces of gravel.'] ['As with all size-based classifications, there is considerable variation in what is considered gravel.'] ['gravel'] +ENVO_01001125 ['An ice is an environmental material which is either frozen or which is maintained in a solid state by gravitational forces or pressure.'] ['Note that ice may be formed at very high temperatures, due to gravitational effects and/or pressure.'] ['ice'] +ENVO_00001995 ['A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids.'] ['From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure.'] ['rock'] +ENVO_00000194 ['Broken rock that appears at the bottom of crags, mountain cliffs or valley shoulders.'] ['scree'] ['TALUS', 'talus slope'] +ENVO_01000660 ['Tephra is fragmental material produced by a volcanic eruption regardless of composition, fragment size or emplacement mechanism.'] ['tephra'] +ENVO_01000256 ['A mineral material is an environmental material which is primarily composed of some substance that is naturally occurring, solid and stable at room temperature, representable by a chemical formula, usually abiogenic, and that has an ordered atomic structure.'] ['mineral material'] "['Look for ""mineral"" in a chemical or geochemical ontology to formalise the composed primarily of link.\nFrom https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure.']" +ENVO_00002008 ['Particulate environmental material with diameters less than 500 micrometers.'] ['Dust occurs in and may be deposited from the atmosphere.'] ['dust'] ['Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.'] +ENVO_00002164 ['A solid environmental material which is formed by the replacement of organic substances (including those in soils and sediments) with mineral material.'] ['fossil material'] +ENVO_01000000 ['Organic matter in soil which has reached a point of stability, where it will break down no further and might, if conditions do not change, remain essentially as it is for centuries, or millennia.'] ['humus'] +ENVO_02000090 ['An environmental material that is the non-aqueous, non-gaseous residues that remain after something is burned.'] ['ash'] +ENVO_01001646 ['A solid material which does not have a regularly organised internal structure.'] ['amorphous solid'] +ENVO_01000480 ['Glass is an amorphous (non-crystalline) solid which is often transparent.'] ['This class refers to all forms of glass. For the familiar form present in window panes and drinking glasses, consider silica-based glass.'] ['glass'] +ENVO_01000560 ['Charcoal is a light, black residue, consisting of carbon and any remaining ash, obtained by removing water and other volatile constituents from animal and vegetation substances. Charcoal is usually produced by slow pyrolysis, the heating of wood or other substances in the absence of oxygen.'] ['charcoal'] +ENVO_01000845 ['A solid material whose constituents, such as atoms, molecules or ions, are arranged in a highly ordered microscopic structure, forming a crystal lattice that extends in all directions.'] ['This class refers to a portion of crystal and not an individual crystal.'] ['crystal'] +ENVO_01001121 ['Organic material which is primarily composed of plant structures, living or dead.'] ['plant matter'] +ENVO_01001231 ['Organic material which is in a solid phase and contained in sedimentary rock.'] ['kerogen'] +ENVO_01001525 ['Frozen soil which is firmly cemented by water ice, is subject to brittle failure, and exhibits practically no consolidation under load.'] ['hard-frozen soil'] +ENVO_01001528 ['Frozen soil which has very low total water content and is not cemented by ice; its compressibility is the same as that of unfrozen soils having the same composition, total water content and density.'] ['dry-frozen soil'] ['friable-frozen soil'] +ENVO_01001561 ['An environmental material which is solid, jelly-like, and exhibits no flow when in steady state material and which contains liquid dispersed in and held in place by cross-linked structures of a solid medium.'] ['gel'] +ENVO_01001850 ['An environmental material which is primarily composed of minute ice crystals forming a fuzzy layer over a cold surface by direct deposition of water vapor.'] "['In British usage, a day on which the minimum temperature at the level of the ground or on the tops of low, close-growing vegetation falls to -0.9C (30.4F) or below (also called a ""day with ground frost""). In more general usage, ""frost"" can refer to the condition that exists when the temperature of the Earth\'s surface and Earthbound objects fall below the melting point of water (0 degrees Celsius or 32 degrees Fahrenheit). Depending upon the actual values of ambient-air temperature, dewpoint, and the temperature attained by surface objects, frost may occur in a variety of forms. These include a general freeze, hoarfrost (or white frost), and dry freeze (or black frost). If a frost period is sufficiently severe to end the growing season (or delay its beginning), it is commonly referred to as a killing frost.']" ['frost'] +ENVO_03501307 ['A solid environmental material that is hard, brittle, heat-resistant and corrosion-resistant, made by shaping and then firing a nonmetallic mineral at a high temperature.'] ['ceramic'] +ENVO_00002122 ['Mud which has elevated concentrations of arsenic.'] ['arsenic-rich mud'] +ENVO_00002133 ['Mud which has no or neglible concentrations of dissolved oxygen.'] ['anoxic mud'] ['anaerobic mud'] +ENVO_00002160 ['Mud which is part of an estuary.'] ['estuarine mud'] +ENVO_00005795 ['Mud which is part of a marine ecosystem.'] ['marine mud'] +ENVO_00005797 ['Mud which constitutes the bed of a lake.'] ['lake bottom mud'] +ENVO_02000019 ['An organic material which is primarily composed of some natural bodily fluid or secretion such as blood, semen, saliva, blood plasma, intracellular and interstitial fluids.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['bodily fluid material'] +ENVO_04000008 ['Organic material in soil, which consists of plant and animal residues at various stages of decomposition, cells and tissues of soil organisms, and substances synthesized by soil organisms.'] ['soil organic matter'] +ENVO_01000063 ['A portion of planktonic material is a portion of environmental material primarily composed of plankton.'] ['planktonic material'] ['See Issue #251. Awaiting class creation in PCO to attempt logical definitions.'] +ENVO_01000156 ['Material derived from a biofilm, an aggregate of microorganisms in which cells adhere to each other and/or to a surface. These adherent cells are frequently embedded within a self-produced matrix of extracellular polymeric substance (EPS). Biofilm EPS, which is also referred to as slime, is a polymeric conglomeration generally composed of extracellular DNA, proteins, and polysaccharides in various configurations.'] ['biofilm material'] +ENVO_01000157 ['Material derived from a microbial mat, a multi-layered sheet of micro-organisms, mainly bacteria and archaea. Microbial mats create a wide range of internal chemical environments.'] ['microbial mat material'] +ENVO_01001103 ['An organic material which is primarily composed of dead particulate matter.'] ['detritus'] +ENVO_01000628 ['Leaf litter is dead plant material, such as leaves, bark, needles, and twigs, that has fallen to the ground.'] ['duff', 'leaf litter', 'litterfall', 'soil litter', 'tree litter'] ['plant litter'] +ENVO_01000349 ['An organic material primarily composed of a portion of plant root.'] ['Requested in Issue 115 as part of the annotation of metagenomic submissions present in the European Nucleotide Archive.'] ['root matter'] +ENVO_02000008 ['A cell culture is a growth of cells in vitro in an artificial medium for experimental research.'] ['cell culture'] +ENVO_01001395 ['Biomass which is composed primarily of dead organisms, their parts, or their organic derivatives.'] ['dead biological matter', 'dead biomass'] ['necromass'] +ENVO_03501304 ['A thin, transparent sheet made of regenerated cellulose.'] ['Cellophane is used for food packaging.'] ['cellophane'] ['Plastic Wrap'] +ENVO_03600084 ['An organic material which is derived from lichen mats.'] ['lichen material'] +ENVO_1000746 ['A gelatinous material primarily composed of exopolymeric compounds with colloidal properties, formed through the aggregation of marine snow particles, often found in large sheets, flocs, and clouds.'] ['The formation of marine mucilage is often associated with conditions which stress marine microorganisms such as diatoms.'] ['marine mucilage'] ['See issue #276.\nThis class is complex as marine mucilage is quite complex. It will also requre new class creation in GO process for deeper semantics.'] ['sea snot'] +ENVO_00002001 ['Water that has been adversely affected in quality by anthropogenic influence.'] ['waste water'] +ENVO_02000022 "[""A bodily fluid material which is composed primarily of excreta, bodily fluids consisting of matter which contains the waste products of biological processes, including urine or feces, discharged from an organism's body.""]" "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['excreta material'] +ENVO_00002267 ['Industrial wastes are liquid, solid and gaseous wastes originating from the manufacture of specific products.'] ['industrial waste material'] "[""This will become a defined class, with subclasses added through inference based on material having a 'waste role' and being associated with industrial entities.""]" ['industrial waste'] +ENVO_01000371 ['Agricultural waste is waste produced as a result of various agricultural operations. It includes manure and other wastes from farms, poultry houses and slaughterhouses; harvest waste; fertilizer run- off from fields; pesticides that enter into water, air or soils; and salt and silt drained from fields.'] ['As with other wastes, this is more a role than a material in itself. This should be revised.'] ['agricultural waste material'] ['agricultural waste'] +ENVO_00002872 ['The biomass remaining after sugarcane stalks are crushed to extract their juice.'] ['sugarcane bagasse'] ['bagasse'] +ENVO_01000373 ['Biological waste is waste containing mostly natural organic materials (remains of plants, animal excrement, biological sludge from waste-water treatment plants and so forth).'] ['biological waste material'] "[""This will become a defined class, with subclasses added through inference based on material having a 'waste role' and being composed primarily of some organic or biological matter.""]" ['biological waste'] +ENVO_01000372 ['Household waste refers to waste material usually generated in the residential environment. Waste with similar characteristics may be generated in other economic activities and can thus be treated and disposed of together with household waste.'] ['household waste material'] "[""This will become a defined class, with subclasses added through inference based on material having a 'waste role' and being associated with domestic entities.""]" ['household waste'] +ENVO_03510070 ['Waste which contains toxic components (e.g., heavy metals or radiation) which can cause harm to organisms and/or the environment.'] ['toxic waste'] +ENVO_03600006 ['A waste material which is primarily composed of uneaten food and removed from the food supply chain.'] ['food loss'] ['The causes of food waste or loss are numerous and can occur during production, processing, distribution, retail and consumption.'] ['food waste'] ['does FoodOn want this?'] +ENVO_01000017 ['Particulate environmental material which is composed primarily of particles of sand with only minor proportions of other substances.'] ['This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider as sands soil material that contains 85% or more sand; the percentage of silt plus 1.5 times the percentage of clay does not exceed 15. coarse sand (sable grossier) 25% or more very coarse and coarse sand, and less than 50% any other one grade of sand.'] ['sand'] ['Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.'] +ENVO_00002007 ['Particulate environmental material which is formed as a result of the transport and deposition of particles by flowing liquid.'] ['Sediment is typically deposited on the bed or bottom of a body of water or other liquid.'] ['sediment'] +ENVO_01001563 ['Particulate environmental material which 1) is primarily composed of a fine, granular material such as sand, silt, or clay suspended in and saturated by water and 2) readily liquefies when weight is applied, losing strength and permitting objects to sink until their weight and buoyancy offset the weight of the displaced quicksand.'] ['quicksand'] ['Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.'] +ENVO_01000016 ['Particulate environmental material which is primarily composed of silt particles.'] ['This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider this soil material that contains 80% or more silt and less than 12% clay. In the Udden-Wentworth scale (due to Krumbein), silt particles range between 0.0039 to 0.0625 mm, larger than clay but smaller than sand particles. ISO 14688 grades silts between 0.002 mm and 0.063 mm. In actuality, silt is chemically distinct from clay, and unlike clay, grains of silt are approximately the same size in all dimensions; furthermore, their size ranges overlap. Clays are formed from thin plate-shaped particles held together by electrostatic forces, so present a cohesion. According to the U.S. Department of Agriculture Soil Texture Classification system, the sand-silt distinction is made at the 0.05 mm particle size. The USDA system has been adopted by the Food and Agriculture Organization (FAO). In the Unified Soil Classification System (USCS) and the AASHTO Soil Classification system, the sand-silt distinction is made at the 0.075 mm particle size (i.e., material passing the #200 sieve). Silts and clays are distinguished mechanically by their plasticity.'] ['silt'] ['Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.'] +ENVO_00002982 ['Particulate environmental material which 1) is composed primarily of clay particles, with only minor proportions of other materials, 2) demonstrates plasticity when wet, and 3) is capable of hardening when dried or fired.'] "[""This definition is intentionally ambiguous to support the multiple thresholds set by different authorities.The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam. Similar mixtures with greater than 40% clay are often considered clay soils.""]" ['clay'] ['Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.'] +ENVO_01000436 ['Particulate environmental material in which small portions of solid material are surrounded by water.'] ['waterborne particulate matter'] "[""This class should be populated by inference, relying on 'composed primarily of', many 'pieces of solid material' and 'surrounded by' some 'water'.""]" +ENVO_03000021 ['Particulate environmental material which is composed primarily of carbon particles formed through the incomplete combustion of hydrocarbons.'] ['soot'] ['Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.'] +ENVO_03000038 ['Particulate environmental material which is composed primarily of dust, rock, and soot, as well as the microbial communities associated with these materials, deposited on an ice mass by an aeolian process.'] ['cryoconite deposit'] ['Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.', 'This actually is formed as a result of an accumulation process involving the constituents of cryoconite. When their semantics are more stable, we can axiomatise this fully.'] +ENVO_04000012 ['Particulate environmental material which is composed primarily of organic material.'] ['particulate organic matter'] ['Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.'] +ENVO_00002170 ['Manure which has been derived from the aerobically decomposed remnants of organic materials.'] ['compost'] +ENVO_00003031 ['Manure which is derived from the waste products of animals.'] "['This is interesting in that the ""role"" aspect of ""waste"" is (or can be) replaced by another role ""fertilizer"". Thus, the positioning of ""manure"" under waste may not be totally correct.']" ['animal manure'] +ENVO_00002985 ['A nonpolar, hydrophobic, and lipophilic material which is a viscous liquid at ambient temperatures (about 20 degrees Celsius) or slightly warmer.'] ['oil'] +ENVO_01000554 ['A gas that is primarily composed of hydrocarbon molecules.'] ['hydrocarbon gas'] +ENVO_01001139 ['Ice which is primarily composed of methane.'] ['methane ice'] +ENVO_01001238 ['Kerogen which has a hydrogen to carbon ratio less than 0.5 and primarily composed of polycyclic aromatic hydrocarbons.'] ['residual kerogen'] +ENVO_00005739 ['A foamy environmental material which 1) is created by the agitation of seawater, 2) whose stability depends on the content of the seawater.'] ['The lifetime of sea foam can vary from only seconds to several hours or days. The longer-lasting foam are formed in particular when seawater contain higher concentration of dissolved organic matter that derived from sources such as algal blooms.'] ['sea foam'] +ENVO_01001089 ['An aerosol which has non-gaseous parts that are primarily composed of solid particles.'] ['solid aerosol'] ['aerosolised solids'] +ENVO_01001088 ['An aerosol which has non-gaseous parts that are primarily composed of liquid droplets.'] ['liquid aerosol'] ['aerosolised liquids'] +ENVO_01001652 ['An aerosol that is suspended in an atmosphere.'] ['atmospheric aerosol'] +ENVO_01000797 ['A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely.'] ['gaseous environmental material'] ['This class is to be populated by inference.'] ['gas'] +ENVO_01000815 ['An environmental material which is in a liquid state.'] ['This is a defined class: most of its subclasses will not be asserted, but filled by inference.'] ['liquid environmental material'] +ENVO_01000231 ['Lava is a mixture of molten or semi-molten rock, volatiles, and solids which has extruded beyond a planetary crust.'] "[""Some use 'lava' to refer to rock that is formed when lava cools. This is not the intended meaning of this class. See 'igneous rock' or similar.""]" ['lava'] +ENVO_01000648 ['Magma is a mixture of molten or semi-molten rock, volatiles, and solids that is found beneath the uppermost solid layer of a planetary body. Besides molten rock, magma may also contain suspended crystals, dissolved gas and sometimes gas bubbles.'] ['magma'] +ENVO_01000798 ['A material entity which is composed of a volume of unbound positive and negative particles in roughly equal numbers, conducts electricity, and possesses internal magnetic fields.'] ['plasma'] ['An NTR for `quality of a plasma` has been posted on the PATO tracker: https://github.com/pato-ontology/pato/issues/88'] +ENVO_03600007 ['A fluid environmental material which is contained in geologic formations naturally.'] ['formation fluid'] ['assert contained in some child of astronmical body part? cavity? Parent class could use a better definition?'] +ENVO_03600082 ['Fluid environmental material which is present in the continental crust and dictates the nature and extent of crustal deformation.'] ['The presence or absence of fluids exerts a fundamental control on rheology.'] ['crustal fluid'] +ENVO_02000118 ['A white or colourless soft solid derivable from petroleum, coal or oil shale, that consists of a mixture of hydrocarbon molecules containing between twenty and forty carbon atoms.'] ['paraffin wax'] +ENVO_02000117 ['A wax that is naturally synthesized by a plant or animal.'] ['natural wax'] +ENVO_01001155 ['An astrogeological volatile which is composed primarily of chemical compounds with boiling points around those of hydrogen and helium.'] ['This is a term native to the fields of planetary science and astrophysics. Hydrogen has a boiling point of 20.271 Kelvin and a melting point of 13.99 Kelvin. Helium has a boiling point of 4.222 Kelvin and a melting point of 0.95 Kelvin.'] ['astrogeological gas'] ['gas'] +ENVO_01001126 ['An astrogeological volatile which is composed primarily of chemical compounds with freezing points above an approximate threshold of 100 Kelvin.'] "['This is a term native to the fields of planetary science and astrophysics. Water, ammonia, and methane are considered ""ices"" with freezing points of 273 K, 195 K, and 91 K, respectively.']" ['astrogeological ice'] ['ice'] +ENVO_01001647 ['A colloidal suspension which is dispersed through a part of a hydrosphere.'] ['colloid suspended in a hydrosphere'] +ENVO_02000047 ['Food material which can be used to meet nutritional requirements of animals, particularly livestock such as cattle, goats, sheep, horses, chickens and pigs.'] ['Most animal feed is from plants but some is of animal origin. Fodder refers particularly to food given to the animals (including plants cut and carried to them), rather than that which they forage for themselves. It includes hay, straw, silage, compressed and pelleted feeds, oils and mixed rations, and also sprouted grains and legumes.'] ['animal feed'] ['fodder'] +ENVO_02000055 ['Food material which can be used to meet nutritional requirements of plants.'] ['plant feed'] +FOODON_00001002 ['Food material for humans and animals which is processed with the intention that it be consumable as a whole or added to other food products.'] "['The FoodOn ""food product"" class is provided as a branch under which new food product categories and food products themselves can be placed. Here classes are provided to differentiate a food product by its food composition, processing and/or consumption characteristics. This avoids brand name products but it may include generic food dish categories. It has a much greater depth and polyhierarchy than other agency product type schemes have in an effort to group related products together. The upper level basis of this tree originated in the environment ontology (ENVO) and from the US Code of Federal Regulations.']" ['food product'] +FOODON_03400361 ['An agency food product type is a class of food product defined by an agency or consortium.'] "[""This class is designed to hold 3rd party food classification schemes which are being mapped to FoodOn classes using the 'has member' relation. The two hierarchies are not melded into a subclass polyhierarchy because of possible logical inconsistencies in the agency schemes. The hierarchies of agency schemes are as true to their agency representation as possible.""]" ['agency food product type'] +ENVO_06105112 ['A plastic which is composed primarily of polymers produced by a manufacturing process.'] ['manufactured plastic'] ['synthetic plastic'] ['The corresponding subclass axiom will be added in the second phase of this project.'] +ENVO_06105016 ['A plastic which has a matrix- or sponge-like structure with numerous, hollow internal spaces.'] ['geschäumter Kunststoff', 'plastic foam'] ['foamed plastic'] ['cellular polymers', 'expanded polymers'] +ENVO_06105111 ['Plastic which is composed primarily of polymers produced by processes whose agents do not include humans or their technologies.'] ['natural plastic'] ['The corresponding subclass axiom will be added in the second phase of this project.'] +ENVO_00002059 ['A treated form of sludge, sometimes used as a fertilizer in agriculture.'] ['biosolids'] +ENVO_00002869 ['Hay is grass, legumes or other herbaceous plants that have been cut, dried, and stored for use as animal fodder, particularly for grazing livestock such as cattle, horses, goats, and sheep.'] ['hay'] +ENVO_00003030 ['A fermented, high-moisture forage that can be fed to ruminants.'] ['silage'] +ENVO_00003869 ['An agricultural byproduct, the dry stalk of a cereal plant, after the nutrient grain or seed has been removed.'] ['straw'] +ENVO_01000473 ['Thatch is material composed of dry vegetation such as straw, water reed, sedge (Cladium mariscus), rushes, or heather.'] "['Some sort of logical definition towards:\ncomposed_primarily_of some ((straw or \'water reed\' or rushes or sedge or heather) and has_quality dry)\nshould be considered, where ""rushes"", ""sedge"", etc are represented as materials rather than some sort of taxon.']" ['thatch'] +ENVO_01001113 ['Material which is primarily conposed of the vegetation present in tended pastures: mainly grasses, with an interspersion of legumes and other forbs.'] ['forage material'] ['forage'] +ENVO_02000053 ['A skin obtained from animals for human use typically from deer or cattle sources used to produce leather, shoes, fashion accessories, musical instruments.'] ['hide'] +ENVO_03000133 ['An agricultural environmental material which 1) is composed of a mixture of materials such as peat, composted bark, sand, perlite, or compost, and 2) serves as a medium in which to grow plants.'] ['potting soil'] ['Potting soil can be composed of a wide range of materials in varying ratios, often containing little or no actual soil.'] ['agricultural potting mixture'] +ENVO_01000459 ['Asphaltic concrete is a concrete which uses refined asphalt as a cement.'] ['asphaltic concrete', 'road pavement'] ['asphalt concrete'] +ENVO_01000463 ['Hydraulic cement is a masonry cement which contains activated aluminium silicates or pozzolans, such as fly ash, allowing it to set in wet conditions or underwater.'] ['hydraulic cement'] +ENVO_01000464 ['Non-hydraulic cement is a cement which sets by reacting with carbon dioxide in the air and will not set in wet conditions or underwater. It is susceptible to attack by aggresive chemicals after setting.'] ['non-hydraulic cement'] +ENVO_01000477 ['Gypsum plaster is a plaster which is formed by partially dehydrating gypsum by heating it to approximately 150 degrees Celsius and grinding the product into a powder. Gypsum anhydride - formed by heating gypsum above 200 degrees Celsius - may also be used as plaster.'] ['plaster of Paris'] ['gypsum plaster'] +ENVO_01000479 ['Lime plaster is a plaster which is primarily composed of calcium hydroxide and an inert filler (such as sand). Coversion of the calcium hydroxide to calcium carbonate through a reaction with carbon dioxide in the air causes the plaster to set.'] ['lime render', 'lime stucco', 'slaked lime plaster'] ['lime plaster'] +ENVO_02000124 ['Paint that contains lead.'] ['lead paint'] +ENVO_03510029 ['A paint product which adheres to surfaces and forms a binding layer, preparing it to receive paint.'] ['primer (paint)'] +ENVO_03510031 ['A slow-drying paint that consists of particles of pigment suspended in a drying oil, commonly linseed oil.'] ['oil paint'] ['oil-based paint'] +ENVO_03510032 ['A water soluble, fast-drying paint made of pigment suspended in acrylic polymer emulsion.'] ['acrylic paint'] +ENVO_03510033 ['A paint that exhibits luminescence, giving off visible light through fluorescence, phosphorescence, or radioluminescence.'] ['luminous paint'] ['luminescent paint'] +ENVO_00005758 ['A portion of alluvial soil which is part of a swamp ecosystem.'] ['alluvial swamp soil'] +ENVO_00005759 ['Alluvial soil whichi is part of a paddy field.'] ['alluvial paddy field soil'] +ENVO_00002116 ['A portion of contaminated soil is a portion of soil with elevated levels of some contaminant.'] "['""contaminant"" is more of a disposition - any material entity can be a contaminant in particular circumstances.']" ['contaminated soil'] +ENVO_00003083 ['A portion of sarcosine enriched soil is a portion of soil with elevated levels of sarcosine.'] ['sarcosine enriched soil'] +ENVO_00003084 ['A portion of trimethylamine enriched soil is a portion of soil with elevated levels of trimethylamine.'] ['trimethylamine enriched soil'] +ENVO_00003085 ['A portion of skatole enriched soil is a portion of soil with elevated levels of skatole.'] ['skatole enriched soil'] +ENVO_00003086 ['A portion of ethanol enriched soil is a portion of soil with elevated levels of ethanol.'] ['ethanol enriched soil'] +ENVO_00003087 ['A portion of acetamide enriched soil is a portion of soil with elevated levels of acetamide.'] ['acetamide enriched soil'] +ENVO_00003088 ['A portion of pantothenate enriched soil is a portion of soil with elevated levels of pantothenate.'] ['pantothenate enriched soil'] +ENVO_00003089 ['A portion of testosterone enriched soil is a portion of soil with elevated levels of testosterone.'] ['testosterone enriched soil'] +ENVO_00003090 ['A portion of kynurenate enriched soil is a portion of soil with elevated levels of kynurenate.'] ['kynurenate enriched soil'] +ENVO_00003091 ['A portion of threonine enriched soil is a portion of soil with elevated levels of threonine.'] ['threonine enriched soil'] +ENVO_00003092 ['A portion of salicylate enriched soil is a portion of soil with elevated levels of salicylate.'] ['salicylate enriched soil'] +ENVO_00003093 ['A portion of poly-beta-hydroxybutyrate enriched soil is a portion of soil with elevated levels of poly-beta-hydroxybutyrate.'] ['poly-beta-hydroxybutyrate enriched soil'] +ENVO_00003094 ['A portion of L-(+)-tartrate enriched soil is a portion of soil with elevated levels of L-(+)-tartrate.'] ['L-(+)-tartrate enriched soil'] +ENVO_00003095 ['A portion of quinate enriched soil is a portion of soil with elevated levels of quinate.'] ['quinate enriched soil'] +ENVO_00003914 ['Soil which has increased levels of chalk.'] ['chalk soil'] +ENVO_00005753 ['A portion of urea enriched soil is a portion of soil with elevated levels of urea.'] ['urea enriched soil'] +ENVO_00005757 ['A portion of bacteria enriched soil is a portion of soil with elevated bacterial abundance.'] ['bacteria enriched soil'] +ENVO_00005762 ['A portion of chloropicrin enriched soil is a portion of soil with elevated levels of chloropicrin.'] ['chloropicrin enriched soil'] +ENVO_00005763 ['Soil which 1) has increased levels of humus, 2) has low pH levels, 3) has increased levels of mineral ash.'] ['humus-rich acidic ash soil'] +ENVO_00005776 ['Paddy field soil which has increased levels of peat.'] ['peaty paddy field soil'] +ENVO_01000427 ['A portion of carbon nanotube enriched soil is a portion of soil with elevated levels of carbon nanotubes.'] "['Logical definition will be created pending import of ""carbon nanotube"" from CHEBI']" ['carbon nanotube enriched soil'] +ENVO_06105274 ['Loam which has a high proportion of sand in its composition.'] ['Some authorities consider sandy loam to be a soil composed of 50-70% sand, 0-50% silt, and 0-20% clay. Others, a soil material that contains either 20% or less clay, with a percentage of silt plus twice the percentage of clay that exceeds 30, and 52% or more sand; or less than 7% clay, less than 50% silt, and between 43% and 52% sand.'] ['sandy loam'] +ENVO_06105275 ['Loam which has a high proportion of silt in its composition.'] ['USDA textural classes of soils', 'Some authorities consider silt loam to be a soil composed of 20-50% of sand, 74-88% silt and 0-27% of clay.'] ['silty loam'] +ENVO_06105277 ['Loam which has a high proportion of clay in its composition.'] ['Some authorities consider clay loam to be a soil composed of 20-45% sand, 15-52% silt, and 27 to 40% clay.'] ['clay loam'] ['Interestingly, some instances of this class may not actually conform to the definition of loam, by having roughly unequal proportions of sand and silt and quite a large proportion of clay.'] +ENVO_01001841 ['An andosol which derives its silica content from glass and tephra ejected during a volcanic eruption.'] ['volcanic soil'] +ENVO_00002234 ['Acrisols are soils that have a higher clay content in the subsoil than in the topsoil as a result of pedogenetic processes (especially clay migration) leading to an argic subsoil horizon. Acrisols have in certain depths a low base saturation and low-activity clays.'] ['acrisol'] +ENVO_00002236 ['Cryosols comprise mineral soils formed in a permafrost environment. Where water is present, it occurs primarily in the form of ice. Cryogenic processes are the dominant soil-forming processes.'] ['cryosol'] ['gelisol'] +ENVO_00005765 ['Compost soil which is frozen.'] ['frozen compost soil'] +ENVO_01001527 ['Frozen soil which is cemented by water ice but has viscous properties due to its high, unfrozen water content and therefore will compress and deform under load.'] ['plastic-frozen soil'] +ENVO_00005774 ['A histosol which is formed by the decomposition of vegetation or organic matter.'] ['peat soil'] ['turf'] ['peat'] +ENVO_00005740 ['Soil which is part of a paddy field.'] ['paddy field soil'] ['rice paddy soil'] +ENVO_00005789 ['Bluegrass field soil is a soil which is found in a field of Kentucky Bluegrass (Poa pratensis).'] ['bluegrass field soil'] +ENVO_00002260 ['Soil which is part of some dune.'] ['dune soil'] +ENVO_00005769 ['Soil which is part of a forest growing on a mountain.'] ['mountain forest soil'] +ENVO_00005770 ['Soil which is part of a forest whose communites of arborescent plants are dominated the genus Fagus.'] ['beech forest soil'] +ENVO_00005783 ['Soil which is part of a woodland dominated by leafy trees.'] ['leafy wood soil'] +ENVO_00005784 ['Soil which is part of a forest whose communites of arborescent plants are dominated the genus Picea.'] ['spruce forest soil'] +ENVO_00005787 ['Soil which is part of a forest whose communites of arborescent plants are dominated the genus Eucalyptus.'] ['eucalyptus forest soil'] +ENVO_00005744 ['Soil which is part of an allotment garden.'] ['allotment garden soil'] +ENVO_00005779 ['Garden soil which is part of a garden used for the cultivation of vegetables.'] ['vegetable garden soil'] +ENVO_00005746 ['A portion of soil which is found in a savanna.'] ['savanna soil'] +ENVO_00005777 ['A portion of soil which is found in a steppe.'] ['steppe soil'] +ENVO_00005772 ['Soil in which trees from an orchard grow.'] ['orchard soil'] +ENVO_01000277 ['Ice which is formed from water.'] "[""Water ice can appear transparent or opaque bluish-white color, depending on the presence of impurities or air inclusions. The addition of other materials such as soil may further alter its appearance.\n\nWhen speaking about ice on Earth, usually water ice is meant - the solid, crystalline form of water found in the atmosphere as snow crystals, hail, ice pellets, etc., and on the earth's surface in forms such as hoarfrost, rime, glaze, sea ice, glacier ice, ground ice, frazil, anchor ice, etc.\n\nThis form of water is, strictly speaking, called ice Ih, the Roman numeral I distinguishing it from more than a dozen other phases and the letter h distinguishing it from the metastable cubic phase ice Ic. Ice Ih is the only one of the several known phases of water ice that is stable at commonly occurring temperatures and pressures. (Some of the other forms have very unusual properties, ice VII, for example, being stable only at pressures above 22 400 kg/cm^2, but then existing at temperatures up to about 100C.)\n\nIt has an open structure with a specific gravity of 0.9166 which is slightly less than water; because the water molecules bond to their neighbors covalently only in four directions; it therefore floats on higher density water, where broken molecular bonds permit closer packing. All commonly occurring forms of ice are crystalline, although large single crystals are relatively rare except in glaciers. The ice crystal lattice possesses hexagonal symmetry that manifests itself in the gross forms of such single crystals as are sometimes found in snow. At an air pressure of one atmosphere, ice melts at 0 C by definition of the Celsius temperature scale. (Strictly speaking the equilibrium point among water, ice, and vapor occurs at +0.01C, the triple point.) On the other hand, ice does not invariably form in liquid water cooled below this temperature; it has a tendency to supercool, more so in the absence of ice nuclei.\n\nIn permafrost regions, ice may occupy voids in soils and rocks and may develop in a variety of forms. Ice may be colourless to pale blue or greenish-blue. It may appear white due to included gas bubbles; in exposures, ground ice may also appear black.\n\nIn nature ice is formed either by: (a) the freezing of water, (b) the condensation of atmospheric water vapour direct into ice crystals, (c) the compaction of snow with or without the motion of a glacier, or (d) the impregnation of porous snow masses with water which subsequently freeze.""]" ['water ice'] ['ice'] +ENVO_01001138 ['Ice which is primarily composed of carbon dioxide.'] ['carbon dioxide ice'] ['dry ice'] +ENVO_01001140 ['Ice which is primarily composed of ammonia.'] ['ammonia ice'] +ENVO_01001141 ['Ice which is primarily composed of carbon monoxide.'] ['carbon monoxide ice'] +ENVO_00002016 ['A rock formed by deposition of either clastic sediments, organic matter, or chemical precipitates (evaporites), followed by compaction of the particulate matter and cementation during diagenesis.'] ['sedimentary rock'] +ENVO_01000662 ['Scoria is a highly vesicular, dark colored volcanic rock that may or may not contain crystals.'] ['cinder'] ['Scoria differs from pumice in having larger vesicles, thicker vesicle walls and being dark colored and denser.'] ['scoria'] +ENVO_01000663 ['Pumice is a volcanic rock that consists of highly vesicular rough textured volcanic glass, which may or may not contain crystals.'] ['Scoria differs from pumice in having larger vesicles, thicker vesicle walls and being dark colored and denser.'] ['pumice'] +ENVO_00002013 ['Rock formed from molten magma.'] ['igneous rock'] +ENVO_00002015 ['An igneous rock that results from magma reaching the surface either as lava or fragmental ejecta.'] "[""Due to the general suggestion that volcanic rock simply comes from a volcanic process, it's not immediately clear whether this is interchangeable with igneous rock.""]" ['volcanic rock'] +ENVO_00002017 "[""A rock formed by subjecting any rock type (including previously-formed metamorphic rock) to different temperature and pressure conditions than those in which the original rock was formed. These temperatures and pressures are always higher than those at the Earth's surface and must be sufficiently high so as to change the original minerals into other mineral types or else into other forms of the same minerals (e.g. by recrystallisation).""]" ['metamorphic rock'] +ENVO_01000751 ['A lithified mass of rock that lies under the loose softer material (regolith) at the surface of the Earth or other terrestrial planet.'] ['bedrock'] +ENVO_01000661 ['Tuff is a type of rock made of volcanic ash ejected from a vent during a volcanic eruption.'] ['tuff'] +ENVO_01001204 ['A rock which is formed as a result of the lithification of alluvium.'] ['alluvial deposit'] +ENVO_02000094 ['a type of rock that contains sufficient minerals with important elements including metals that can be economically extracted from the rock.'] ['ore'] +ENVO_03600016 ['Rock which is derived from bedrock through chemical weathering'] ['saprolite'] ['add chemcical weathering term to improve axiomitization'] +ENVO_01000853 ['Marl is a mass of calcium carbonate derived from mollusk shells and mixed with silt and clay.'] ['marl'] ['A request from the Agronomy Ontology in Issue #345.'] +ENVO_02000100 ['Dust which is derived from mineral material.'] ['mineral dust'] +ENVO_01001282 ['Dust which is composed primarily of slicon dioxide.'] ['silica dust'] +ENVO_01001283 ['Dust which is primarily composed of aluminium particles.'] ['aluminium dust'] +ENVO_01001284 ['Dust which is primarily composed of barium particles.'] ['barium dust'] +ENVO_01001285 ['Dust which is primarily composed of hydrated magnesium silicate (talc) particles.'] ['talc dust'] +ENVO_01001286 ['Dust which is primarily composed of slate particles.'] ['slate dust'] +ENVO_02000099 ['Dust which is derived from coal.'] ['coal dust'] +ENVO_02000101 ['Dust which is composed of fibrous material.'] ['fibrous dust'] +ENVO_02000103 ['Dust which is composed primarily of some metallic material.'] ['metallic dust'] +ENVO_02000105 ['Dust which is derived from clay material.'] ['clay dust'] +ENVO_03510000 ['Dust which is 1) generated when wood is processed and 2) composed primarily of cellulose, polyoses, and lignin.'] ['Wood dust is typically generated through processes where wood is chipped, sawed, turned, drilled or sanded. The chemical composition of wood dust depends on the species of tree. Wood dust is not typically produced for specific uses. However, it is used commercially for wood composts. The primary routes of potential human exposure to wood dust are inhalation and dermal contact. It is known to be a human carcinogen.'] ['wood dust'] +ENVO_03510036 ['Dust which is composed of minerals and trace elements, generated by finely crushed rock.'] ['rock powder'] ['Rock dust is widely used in mining to prevent coal dust explosions, or in agriculture for organic farming uses.'] ['rock dust'] ['mineral fines', 'rock flour', 'soil remineralization'] +ENVO_01000701 ['Volcanic ash is an environmental material which consists of fragments of pulverized rock, minerals, and volcanic glass, created during volcanic eruptions and measuring less than 2 millimetres in diameter. Volcanic ash is formed during explosive volcanic eruptions, phreatomagmatic eruptions and during transport in pyroclastic density currents.'] ['volcanic ash'] +ENVO_02000126 ['the residue powder that is derived from the combustion of wood.'] ['wood ash'] +ENVO_02000127 ['Ash that is produced from the burning of coal.'] ['coal combustion residuals'] ['coal ash'] +ENVO_01000405 ['A portion of respirable suspended particulate matter is a form of particulate matter composed primarily of solid particles each with a diameter of 10 micrometers or less.'] ['PM10'] ['respirable suspended particulate matter'] +ENVO_01000481 ['Silica-based glass is a glass composed primarily of silicon dioxide, the primary constituent of sand.'] ['Silica-based glasses are the most common manufactured variety of glass.'] ['silica-based glass'] ['glass'] +ENVO_2000007 ['charcoal that is used as a soil amendment.'] ['biochar'] +ENVO_01000846 ['A crystal which is primarily composed of water ice.'] ['Any one of a number of macroscopic, crystalline forms in which ice appears, including hexagonal columns, hexagonal platelets, dendritic crystals, ice needles, and combinations of these forms. The crystal lattice of ice is hexagonal in its symmetry under most atmospheric conditions.'] ['water ice crystal'] ['ice crystal'] +ENVO_01000850 ['A material which is primarily composed of a substance arranged as a lattice which can trap or contain other molecules.'] ['clathrate compound material', 'clathrate crystal material'] "['This class is not to be confused with CHEBI\'s ""clathrate"". The latter refers to the pure substance, while this class refers to clathrates found in nature.\n""Traditionally, clathrate compounds are polymeric and completely envelop the guest molecule, but in modern usage clathrates also include host-guest complexes and inclusion compounds."" https://en.wikipedia.org/wiki/Clathrate_compound']" ['clathrate material'] ['Not sure if this should be a subclass of crystal. If it is removed, remember to assert that it is a solid.'] +ENVO_03501302 ['Plant matter consisting of an impermeable buoyant material, the phellem layer of bark tissue.'] ['cork'] +ENVO_01001232 ['Kerogen which cotains alginite, amorphous organic matter, cyanobacteria, freshwater algae, and land plant resins, thus having a hydrogen to carbon ratio above 1.25, and oxygen to carbon ratio below 0.15, readily produces liquid hydrocarbons, has reduced concentrations of aromatic structures, and primarily derived from proteins and lipids.'] ['sapropelic kerogen'] +ENVO_01001233 ['Kerogen from which heavy hydrocarbons (such as oils) are derived following chemical break down.'] ['labile kerogen'] +ENVO_01001234 ['Kerogen from which light hydrocarbons (such as hydrocarbon gases) are derived following chemical break down.'] ['recalcitrant kerogen'] +ENVO_01001235 ['Kerogen which is enriched in sulfur compounds, has a hydrogen to carbon ratio under 1.25, an oxygen to carbon ratio between 0.03 and 0.18, derives into mixtures of hydrocarbon gas and oil, and derives from marine organic materials (primarily lipids) which are formed in reducing environments.'] ['planktonic kerogen'] +ENVO_01001237 ['Kerogen which derives from land plants, resembles wood or coral in structure, has a hydrogen to carbon ratio under 1, an oxygen to carbon ratio between 0.03 to 0.3, and which primarily produces coal or hydrocarbon gas on degradation.'] ['humic kerogen'] +ENVO_01001562 ['A gel which is primarily composed of a network of polymer chains that are hydrophilic, sometimes found as a colloidal gel in which water is the dispersion medium.'] ['hydrogel'] +ENVO_01001845 ['Frost which is composed of interlocking ice crystals formed by vapour transfer (sublimation followed by deposition) of water vapour on some surface.'] ['hoar frost', 'white frost'] ['hoar'] +ENVO_01001848 ['Water ice which 1) has a white or milky and opaque appearance, 2) has a granular texture, and 3) is formed as a result of the deposition and rapid freezing of supercooled water drops as they make contact with an exposed object.'] ['Rime is denser and harder than hoarfrost, but lighter, softer, and less transparent than glaze. Rime is composed essentially of discrete ice granules and has densities as low as 0.2-0.3 g cm-3. Glaze is generally continuous but with some air pockets and has much higher densities. Factors that favor rime formation are small drop size, slow accretion, a high degree of supercooling, and rapid dissipation of latent heat of fusion. The opposite effects favor glaze formation. Both rime and glaze occur when supercooled water drops strike an object at a temperature below freezing. Such formation on terrestrial objects constitutes an ice storm; on aircraft, it is called aircraft icing (where rime is known as rime ice). Either rime or glaze may form on snow crystals, droxtals, or other ice particles in the atmosphere. When such a deposit is wholly or chiefly of rime, snow pellets result; when most or all of the deposit is glaze, ordinary hail or ice pellets result. The alternating clear and opaque layers of some hailstones represent glaze and rime, deposited under varying conditions around the growing hailstone.'] ['rime'] ['The previously use definition was: Frost which is 1) composed primarily of granular ice tufts, 2) formed on the windward sides of exposed objects through contact with supercooled fog or cloud, and 3) built out directly against the wind.'] +ENVO_00000338 ['A bodily fluid material which is composed primarily of vomit, a bodily fluid consisting of the expulsed contents of the stomach of an organism disgorged through the mouth or nose.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['vomit material'] +ENVO_02000020 "[""A bodily fluid material which is composed primarily of blood, a bodily fluid composed of blood plasma and blood cells suspended within the plasma that circulates around the organism's body. Blood performs may important functions including the supplying of oxygen and nutrients, removal of waste, circulation of white blood cells, detection of antibodes, coagulation, transportation of antibodies and the regulation of pH and body temperature.""]" "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['blood material'] +ENVO_02000021 ['A bodily fluid material which is composed primarily of amniotic fluid, a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['amniotic fluid material'] +ENVO_02000023 ['A bodily fluid material which is composed primarily of bile, a bodily fluid consisting of a bitter, yellow or green alkaline fluid secreted by hepatocytes from the liver of most vertebrates. In many species, bile is stored in the gallbladder between meals and upon eating is discharged into the duodenum where the bile aids the process of digestion of lipids.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['bile material'] ['gall'] +ENVO_02000024 ['A bodily fluid material which is composed primarily of aqueous humour, a bodily fluid consisting of a thick watery substance that fills the space between the lens and the cornea.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['aqueous humour material'] +ENVO_02000026 ['A bodily fluid material which is composed primarily of chyme, a bodily fluid consisting of a liquid substance found in the stomach before passing through the pyloric valve and entering the duodenum. It results from the mechanical and chemical breakdown of a bolus and consists of partially digested food, water, hydrochloric acid, and various digestive enzymes.'] ['chymus'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['chyme material'] +ENVO_02000027 ['A bodily fluid material which is composed primarily of blood plasma, a bodily fluid that comprises the liquid component of blood, in which the blood cells are suspended. It makes up about 55% of total blood volume.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['blood plasma material'] +ENVO_02000028 ['A bodily fluid material which is composed primarily of ear wax, a bodily fluid consisting of a yellowish, waxy substance secreted in the ear canal of humans and many other mammals. It plays an important role in the human ear canal, assisting in cleaning and lubrication, and also provides some protection from bacteria, fungi, and insects.'] ['cerumen material'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['ear wax material'] +ENVO_02000029 ['A bodily fluid material which is composed primarily of cerebrospinal fluid, a clear bodily fluid that occupies the subarachnoid space and the ventricular system around and inside the brain. CSF is a clear bodily fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.'] ['CSF material'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['cerebrospinal fluid material'] ['Liquor cerebrospinalis'] +ENVO_02000030 ['A bodily fluid material which is composed primarily of chyle, a bodily fluid consisting of a milky fluid consisting of lymph and emulsified fats; formed in the small intestine during digestion of ingested fats.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['chyle material'] +ENVO_02000031 "[""A bodily fluid material which is composed primarily of breast milk, is a bodily fluid produced that is secreted from two milk-secreting glandular organs on a female's chest.""]" "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['breast milk material'] +ENVO_02000032 ['A bodily fluid material which is composed primarily of vitreous humor, a bodily fluid consisting of a clear gel that fills the space between the lens and the retina of the eyeball of humans and other vertebrates.'] ['vitreous humour material'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['vitreous humor material'] +ENVO_02000033 ['A bodily fluid material which is composed primarily of a pleural effusion, a bodily fluid that is produced in excess and accumulates in the pleural cavity, the fluid-filled space that surrounds the lungs. Excessive amounts of such fluid can impair breathing by limiting the expansion of the lungs during inhalation.'] ['pleural effusion material'] +ENVO_02000034 ['A bodily fluid material which is composed primarily of a volume of tears, a bodily fluid consisting of a drop of the clear salty liquid secreted by glands (lacrimal glands) in the eyes. Tears wet the membrane covering the eye and help rid the eye of irritating substances.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['tear material'] +ENVO_02000035 ['A bodily fluid material which is composed primarily of an oronasal secretion, a bodily fluid secreted from the body via the mouth or nose.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['oronasal secretion material'] +ENVO_02000036 ['A bodily fluid material which is composed primarily of saliva, a slightly alkaline secretion of water, mucin, protein, salts, and often a starch-splitting enzyme (as ptyalin) that is secreted into the mouth by salivary glands, lubricates ingested food, and often begins the breakdown of starches.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['saliva material'] +ENVO_02000037 ['A bodily fluid material which is composed primarily of sebum, an oily bodily fluid secreted from the sebaceous glads that is made of fat (lipids) and the debris of dead fat-producing cells. In the glands, sebum is produced within specialized cells and is released as these cells burst. Sebum acts to protect and waterproof hair and skin, and keep them from becoming dry, brittle and cracked. It can also inhibit the growth of microorganisms on skin.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['sebum material'] +ENVO_02000038 ['A bodily fluid material which is composed primarily of pus, a bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections. Pus is produced from the dead and living cells which travel into the intercellular spaces around the affected cells.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['pus material'] +ENVO_02000039 ['A bodily fluid material which is composed primarily of synovial fluid, a bodily fluid secreted by the synovial membrane into the joint cavity to form a thin layer at the surface of cartilage.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['synovial fluid material'] +ENVO_02000040 ['A bodily fluid material which is composed primarily of mucus, a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['mucus material'] +ENVO_02000041 ['A bodily fluid material which is composed primarily of lymph, a bodily fluid consisting of a usually clear coagulable fluid that passes from intercellular spaces of body tissue into the lymphatic vessels, is discharged into the blood by way of the thoracic duct and right lymphatic duct, and resembles blood plasma in containing white blood cells and especially lymphocytes but normally few red blood cells and no platelets.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['lymph material'] +ENVO_02000042 ['A bodily fluid material which is composed primarily of interstitial fluid, a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid.'] ['intercellular fluid material', 'tissue fluid material'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['interstitial fluid material'] +ENVO_03605000 ['Biofilm consisting of a mixture of algae, cyanobacteria, microbes, and detritus.'] ['Periphytic biofilm coats the submerged surfaces in most bodies of water'] ['periphytic biofilm'] ['Periphyton'] +ENVO_01000158 ['Marine snow is a continuous shower of mostly organic detritus falling from the upper layers of the water column. Its origin lies in activities within the productive photic zone.'] ['marine snow'] +ENVO_01001059 ['A cell culture which is composed of a microbial community of known composition.'] ['Mock communities are typically used as positive controls in experiments.'] ['mock community culture'] +ENVO_01001060 ['A cell culture which is composed of a single population of bacterial or archaeal cells.'] ['single strain cell culture'] +ENVO_00002018 ['Wastewater that is contaminated with feces or urine,'] ['sewage'] +ENVO_01000964 ['Wastewater which is produced by industrial activity and which contains chemical contaminants other than those associated with urine and fecal matter.'] ['industrial wastewater'] +ENVO_00002003 "[""An excreta material which is composed primarily of feces, an excreta consisting of waste products expelled from an animal's digestive tract through the anus (or cloaca) during defecation.""]" ['faeces material', 'feces material'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.', ""This is distinct from classes such as http://purl.obolibrary.org/obo/UBERON_0001988 in that it refers to the environmental material composed primarily of feces rather than 'just' feces.""]" ['fecal material'] ['droppings', 'frass', 'pellet'] +ENVO_00002047 ['An excreta material which is composed primarily of urine, a liquid excreta containing water and waste products made by the kidneys, stored in the bladder, and leaves the body through the urethra.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['urine material'] +ENVO_02000025 ['An excreta material which is composed primarily of sweat, an excreta consisting primarily of water as well as a smaller amount of sodium chloride that is excreted by the sweat glands in the skin of mammals.'] "['ENVO bodily fluid classes differ from UBERON\'s treatment of bodily fluids. UBERON refers to the substance itself (""S""). We assert that UBERON\'s classes are the primary compositional component of the terms in ENVO (""S material""). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S.']" ['sweat material'] +ENVO_00005800 ['Sand which is part of a desert.'] ['desert sand'] +ENVO_01000350 ['Autoclaved sand is sand that has been sterlised by exposure to high pressure saturated steam at at least 121 degrees Celsius.'] ['Requested in Issue 116 as part of the annotation of metagenomic submissions present in the European Nucleotide Archive.\n'] ['autoclaved sand'] +ENVO_06105272 ['Soil which is primarily composed of sand with silt and clay in progressively smaller proportions.'] ['Some authorities consider this a soil type, composed of 70-86% of sand, 0-30% of silt and 0-15% of clay. Others consider this a soil material that contains at the upper limit 85 to 90% sand, and the percentage of silt plus 1.5 times the percentage of clay is not less than 15, at the lower limit it contains not less than 70 to 85% sand, and the percentage of silt plus twice the percentage of clay does not exceed 30.'] ['loamy sand'] +ENVO_06105273 ['Sand which is composed primarily of fine particles.'] "['Thresholds for what particle size is considered ""fine"" vary by region and authority, as well as the tolerance for proportions of other particle sizes.']" ['fine sand'] +ENVO_00000546 ['Lake sediment is sediment which covers the bottom of a lake. Lake sediments are comprised mainly of clastic material (sediment of clay, silt, and sand sizes), organic debris, chemical precipitates, or combinations of these.'] ['lake sediment'] ['SedimentLayer'] +ENVO_00002045 ['Sediment characterised by the absence of oxygen.'] ['anoxic sediment'] ['anaerobic sediment'] +ENVO_03000033 ['Sediment which has been transported through the marine water column, settling on the seafloor.'] ['marine sediments'] ['Particles of marine sediment are primarily generated by 1) processes in terrestrial systems and transported to the marine realm by the action of rivers or aeolian processes (amongst other routes) , 2) marine organisms, 3) chemical processes in seawater, or 4) cosmogeneous input.'] ['marine sediment'] +ENVO_00002114 ['Sediment which has increased levels of one or more chemical compounds.'] ['chemically enriched sediment'] +ENVO_01000070 ['Sediment comprised of weathered continental rocks, wind blown dust, volcanic ash or other terrestrial material.'] ['terrigenous sediment'] +ENVO_01000082 ['Biogenous sediment is derived from living organisms, typically planktonic organisms possessing shells, frustules or coccoliths.'] ['biogenous sediment'] +ENVO_01000110 ['Hydrogenous sediment is derived from solutes that precipitate out of sea water by a variety of chemical reactions. These are typically less abundant than other sediment types.'] ['hydrogenous sediment'] +ENVO_01000111 ['Cosmogenous sediment is derived from extraterrestrial dust and debris in the form of meteorites and similar entities.'] ['cosmogenous sediment'] +ENVO_01000113 ['Suspended sediment, or suspended load, is the term for the particles settle slowly enough to be carried in flowing water (such as a stream or coastal area) either without touching the bed or while only intermittently touching it. These particles are generally of the fine sand, silt and clay size, although larger particles may be carried as well depending on the intensity of the flow.'] ['suspended sediment'] +ENVO_01000114 ['Sediment characterised by an average particle diameter greater than 256 mm.'] ['boulder sediment'] +ENVO_01000115 ['Sediment characterised by an average particle diameter between 64 and 256 mm.'] ['cobble sediment'] +ENVO_01000116 ['Sediment characterised by an average particle diameter between 4 and 32 mm.'] ['pebble sediment'] +ENVO_01000117 ['Sediment characterised by an average particle diameter between 2 and 4 mm.'] ['granular sediment'] +ENVO_01000118 ['Sediment characterised by an average particle diameter between 62.5 micrometers and 2 mm.'] ['sandy sediment'] +ENVO_01000119 ['Sediment characterised by an average particle diameter between 3.9 and 62.5 micrometers.'] ['silty sediment'] +ENVO_01000120 ['Sediment characterised by an average particle diameter between 1 and 3.9 micrometers.'] ['clay sediment'] +ENVO_01000121 ['Sediment characterised by an average particle diameter below 1 micrometer.'] "['Note that by the particle-size-based definition used here, colloidal sediment need not actually be a colloid. If that is the case, please use ""suspended colloidal sediment"".']" ['colloidal sediment'] +ENVO_01000131 ['Sediment characterised by a temperature of 15-45 degrees Celsius and high-to-low oxygenation. Often impacted by hydrothermal fluid flows.'] ['mesophilic sediment'] +ENVO_01000132 ['Sediment characterised by a temperature of 45-75 degrees Celsius and low to no oxygen content. Often impacted by hydrothermal fluid flows.'] ['thermophilic sediment'] +ENVO_01000133 ['Sediment characterised by a temperature of 80-125 degrees Celsius and no oxygen content. Often impacted by hydrothermal fluid flows.'] ['hyperthermophilic sediment'] +ENVO_01001028 ['Sediment which has its porespace filled by water which has very low levels of sodium chloride and/or other salts.'] ['We do not specify numeric thresholds for saline vs. non-saline here, as this is variable. Consider specifying this on the information and/or data layer for your purposes. If you require an ENVO class with a fixed threshold, please request one using our issue tracker.'] ['sediment permeated by freshwater'] +ENVO_01001036 ['Sediment which has its porespace filled by water with increased levels of sodium chloride and other salts.'] ['We do not specify numeric thresholds for saline vs. non-saline here, as this is variable. Consider specifying this on the information and/or data layer for your purposes. If you require an ENVO class with a fixed threshold, please request one using our issue tracker.'] ['sediment permeated by saline water'] +ENVO_01001203 ['Sediment which has been transported by flowing water and redeposited in a non-marine setting.'] ['alluvial sediment'] +ENVO_01001821 ['Sediment through which hydrothermally modified fluids flow, altering its properties through interaction with their own.'] ['hydrothermally-influenced sediment'] +ENVO_01001396 ['Clay which is part of an abyssal plain.'] ['abyssal clay'] +ENVO_06105279 ['Clay which has a high proportion of sand in its composition.'] "['Some authorities consider sandy clay to be a soil composed of 45-65% of sand, 0-20% of silt and 35-55% of clay. If the proportion of sand exceeds that of clay, it is unclear whether this is still considered clay (due to other properties) or whether a new class ""clay sand"" should be created.']" ['sandy clay'] "[""If this is a soil (in which case the differntia must be made clear) it should be moved (or a new class created) and labelled 'sandy clay soil'.""]" +ENVO_06105280 ['Clay which has a high proportion of silt in its composition.'] "['Some authorities consider this a soil composed of 0-20% of sand, 40-60% of silt and 40-60% of clay. If the proportion of silt exceeds that of clay, it is unclear whether this is still considered clay (due to other properties) or whether a new class ""clay silt"" should be created.']" ['silty clay'] "[""If this is a soil (in which case the differntia must be made clear) it should be moved (or a new class created) and labelled 'silty clay soil'.""]" +ENVO_01001651 ['Waterborne particulate matter which is part of a hydrosphere.'] ['particulate matter in a hydrosphere'] +ENVO_04000013 ['Particulate organic matter which is composed primarily of carbon.'] ['particulate organic carbon'] +ENVO_04000014 ['Particulate organic matter which is composed primarily of nitrogen.'] ['particulate organic nitrogen'] +ENVO_00003033 ['A compost which generally consists of a combination of wheat straw, dried blood, horse manure and ground chalk, composted together and is the residual compost waste generated by industrial mushroom production.'] ['mushroom compost'] +ENVO_00003860 ['Manure which is primarily composed of pig feces.'] ['pig manure'] +ENVO_01001116 ['Manure which has been collected directly or indirectly from dairy cattle, as from flushing of manure from concrete feed lanes, free stalls, and milking facilities.'] ['bovine dairy liquid manure'] +ENVO_01001117 ['Manure which is composed primarily of the feces of poultry.'] ['poultry manure'] +ENVO_01001118 ['Manure which has been subjected to heat treatment for solidification and/or sterilization purposes.'] ['heat-treated animal manure'] +ENVO_01001119 "[""Manure which has been subjected to a natural process of 'rotting' or decomposition of its organic matter content by microorganisms under controlled conditions.""]" ['composted animal manure'] +ENVO_00002984 ['A naturally occurring flammable liquid consisting of a complex mixture of hydrocarbons of various molecular weights and other liquid organic compounds, that are found in geologic formations beneath the planetary surfaces.'] ['petroleum'] ['crude oil'] +ENVO_00002983 ['An oil which 1) is liquid at room temperature (approximately 20 degrees Celsius) 2) is intended to be burned in a furnace or boiler for the generation of heat or used in an engine for the generation of power, 3) is obtained from petroleum distillation, either as a distillate or a residue, 4) composed of long hydrocarbon chains, particularly alkanes, cycloalkanes and aromatics.'] ['furnace oil', 'heavy oil', 'marine fuel'] ['Oils having a flash point of approximately 42 degrees Celsius and oils burned in cotton or wool-wick burners are not typically considered fuel oils. The term fuel oil is also used in a stricter sense to refer only to the heaviest commercial fuel that can be obtained from crude oil, i.e., heavier than gasoline and naphtha.'] ['fuel oil'] +ENVO_01000552 ['Natural gas is a hydrocarbon gas mixture consisting primarily of methane, but commonly includes varying amounts of other higher alkanes and sometimes a usually lesser percentage of carbon dioxide, nitrogen, and/or hydrogen sulfide. Natural gas is a fossil fuel formed when layers of buried plants and gases are exposed to intense heat and pressure over thousands of years.'] ['natural gas'] +ENVO_01000556 ['Biogas is a mixture of different gases produced by the breakdown of organic matter in the absence of oxygen, is primarily composed of methane and carbon dioxide, and may have small amounts of hydrogen sulfide, water, and siloxanes.'] ['This is distinct from natural gas which is a fossil fuel product.'] ['biogas'] +ENVO_01000553 ['Liquified petroleum gas or liquid petroleum gas (LPG or LP gas), also referred to as simply propane or butane, are flammable mixtures of hydrocarbon gases used as fuel in heating appliances, cooking equipment, and vehicles.'] ['LP gas', 'LPG', 'liquid petroleum gas'] ['liquefied petroleum gas'] ['liquified natural gas'] +ENVO_01000557 ['Liquefied natural gas (LNG) is natural gas (predominantly methane, CH4) that has been converted to liquid form for ease of storage or transport. It takes up about 1/600th the volume of natural gas in the gaseous state. It is odorless, colorless, non-toxic and non-corrosive. LNG achieves a higher reduction in volume than compressed natural gas (CNG) so that the (volumetric) energy density of LNG is 2.4 times greater than that of CNG or 60 percent of that of diesel fuel.'] ['liquified natural gas', 'LNG'] ['liquefied natural gas'] +ENVO_01001402 ['An aersolised mass of dust, smoke, or other dry particulates which scatters visible light thus obsscuring visibility through an atmosphere.'] ['haze'] +ENVO_03000139 ['Fog which is composed of particles of ice.'] ['frozen fog', 'ice-crystal fog', 'pogonip'] ['The suspended particles may be partly ice crystals 20 to 100 micron in diameter, but chiefly, especially when dense, droxtals 12-20 micron in diameter. Ice fog is formed by direct freezing of supercooled water droplets with little growth directly from the vapor. It occurs at very low temperatures, and usually in clear, calm weather in high latitudes. The sun is usually visible and may cause halo phenomena or luminous pillars. Ice fog is rare at temperatures warmer than -30 °C, and increases in frequency with decreasing temperature until it is almost always present at air temperatures of -45 °C in the vicinity of a source of water vapor. Such sources are the open water of fast-flowing streams or of the sea, herds of animals, volcanoes, and especially products of combustion for heating or propulsion. At temperatures warmer than -30 °C, these sources can cause steam fog of liquid water droplets, which may turn into ice fog when cooled.'] ['ice fog'] ['In future will add computable renditions of size and temperature constraints. The synonyms of this class can be quite confusing, as they reference entities like frost (which requires a surface for deposition). Might need to add a new droxtal class see https://glossary.ametsoc.org/wiki/Droxtal.'] ['air hoar', 'frost flakes', 'frost fog', 'rime fog'] +ENVO_01000844 ['A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body.'] "['Fog is more opaque than mist, reducing visibility to under one kilometre. This class refers only to fog formed by materials primarily composed of water. ""Fog can be considered a type of low-lying cloud and is heavily influenced by nearby bodies of water, topography, and wind conditions. In turn, fog has affected many human activities, such as shipping, travel, and warfare."" https://en.wikipedia.org/wiki/Fog']" ['fog'] ['haar'] +ENVO_01001458 ['A visible mass of water droplets or ice crystals suspended in the air at or near a planetary surface, formed when humid air cools rapidly.'] ['This class refers only to mist formed by materials primarily composed of water. Mist is less dense than fog, and visibility is typically greater than one kilometre.'] ['mist'] +ENVO_00002005 ['The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth.'] ['air'] +ENVO_01000266 ['Water vapour is a vapour which is the gas phase of water.'] ['aqueous vapor', 'aqueous vapour', 'water vapor'] ['Perhaps a better relation between water vapour and water can be found in or added to RO?'] ['water vapour'] +ENVO_01000451 ['Atmospheric carbon dioxide is an environmental material composed of carbon dioxide in its gaseous form present in an atmosphere.'] ['This could also be considered a part of an environmental material like air.'] ['atmospheric carbon dioxide'] +ENVO_01000537 ['Atmospheric ozone is an environmental material primarily composed of ozone in its gaseous form and present in an atmosphere.'] ['atmospheric ozone'] ['atmospheric ozone'] +ENVO_01000789 ['A portion of gas which is emitted by a fire or other exothermic reaction, is of increased temperature, and typically emits light in the visible range.'] ['flame'] +ENVO_02000112 ['A gas, smoke, or vapor that smells strongly or is dangerous to inhale.'] ['fume'] +ENVO_03510008 ['A gas which results from the incomplete or complete combustion of diesel fuel.'] ['diesel exhaust'] +ENVO_03510009 ['A gas which results from the complete or incomplete combustion of gasoline fuel.'] ['gasoline exhaust'] +ENVO_00002006 ['An environmental material primarily composed of dihydrogen oxide in its liquid form.'] ['liquid water'] ['water'] +ENVO_03510065 ['A liquid environmental material which 1) contains at least one substance which can act as a chemical colorant.'] ['colorant fluid'] +ENVO_01000232 ['Felsic lava is lava which is high in silica (> 69 percent by weight), aluminium, potassium, sodium, and calcium, forming a polymerized liquid rich in feldspar and quartz. Felsic lava has a higher viscosity than other magma types. Felsic magmas can erupt at temperatures as low as 650 to 750 °C. Unusually hot (>950 °C) rhyolite lavas, however, may flow for distances of many tens of kilometres'] ['silicic lava'] ['felsic lava'] +ENVO_01000233 ['Intermediate lava is lava which, relative to felsic lava, is lower in aluminium and silica (between 52 and 63 percent by weight), and usually somewhat richer in magnesium and iron. The temperature of intermediate lava ranges from 750 to 950 degrees Celsius, destroying polymerized bonds and promoting more fluid behaviour relative to felsic lavas and also a greater tendency to form phenocrysts. Higher iron and magnesium tends to manifest as a darker groundmass, and also occasionally amphibole or pyroxene phenocrysts.'] ['andesitic lava'] ['intermediate lava'] +ENVO_01000234 ['Mafic lava is lava which, relative to other lava types other than ultramafic lava, has a high ferromagnesian content and low aluminium and silica content, with silca making up between 45 and 52 percent of its weight.'] ['Mafic lava generally erupts at temperatures in excess of 950 degrees Celsius. The high temperature and low polymerisation in mafic lava favors low viscosity and chemical diffusion, promoting the formation of large, well-formed phenocrysts.'] ['mafic lava'] ['basaltic lava'] +ENVO_01000235 ['Lava which, relative to other lava types, has very high magnesium oxide content and less than 45 percent silica by weight.'] ['Ultramafic lava generally erupts at temperatures of 1600 degrees Celsius. Due to its high temperature and composition, the viscosity of ultramafic lava is very low.'] ['ultramafic lava'] +ENVO_01000444 ['Lava which is high in silica and low in alkali metal oxides.'] ['Rapid solidification of this lava forms dacite.'] ['dacitic lava'] +ENVO_01001515 ['Freshwater ice which forms on a solid substrate through the freezing of freshwater.'] ['freshwater congelation ice'] +ENVO_01001648 ['Colloidal sediment which is suspended in a part of the hydrosphere.'] ['suspended colloidal sediment'] +ENVO_02000048 ['Contaminated animal feed is an animal feed that has become contaminated with or come contact with microorganisms or toxic chemicals.'] ['contaminated animal feed'] +ENVO_02000054 ['A mixture of crushed and coarsely ground bones that is used as an organic fertilizer for plants and formerly in animal feed.'] ['bone meal'] +FOODON_00002381 ['A food product consisting of food material derived primarily from a single organism.'] ['food product by organism'] +FOODON_00002645 ['A food product organized by the process which it results from.'] ['food product by process'] +FOODON_00001714 ['A food product which normally exists as an ingredient to another food product, rather than eaten on its own, and is more complex than a chemical food component.'] ['food product component'] +FOODON_00002373 "[""A meal type is the name of an eating occasion that may have location, food type, or other customary contextual features. (Damion's 1st draft definition)""]" ['food product by meal type'] +FOODON_00001180 ['Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked.'] ['prepared food product'] ['prepared'] +FOODON_00002501 ['A food product consisting of food material derived from ingredients sourced from multiple organisms.'] "[""The definition of this is being discussed in issue: https://github.com/FoodOntology/foodon/issues/57\n\nNamely, how to characterize the threshold of ingredients that make for multi-component classification? Salt, pepper, spices wouldn't normally make a food multi-component?""]" ['multi-component food product'] +FOODON_00002454 "['A class which contains food product categories qualified by a quality such as granularity or temperature, 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.']" ['food product by quality'] +FOODON_03400289 ['Food group having common consumption, functional or manufacturing characteristics, e.g. *FRUIT OR VEGETABLE PRODUCT*, *DAIRY PRODUCT*, *CONFECTIONARY*, *PREPARED FOOD PRODUCT*, etc. [FDA CFSAN 1995]'] ['LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term.'] ['USA agency food product type'] +FOODON_03400352 ['Renamed from *PRODUCT TYPE, CODEX ALIMENTARIUS* in LanguaL 2008.'] ['LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term.'] ['international agency food product type'] +ENVO_03501305 ['Synthetic plastic which is composed of a glossy, moistureproof membrane made of rubber hydrochloride.'] ['pliofilm'] +ENVO_00002060 ['A solid or gel in motor oil caused by the oil gelling or solidifying, usually at temperatures lower than 100deg C.'] ['oil sludge'] +ENVO_00002117 ['Soil which has elevated concentrations of creosote.'] ['creosote contaminated soil'] +ENVO_00003081 ['Soil which has elevated concentrations of metals.'] ['metal contaminated soil'] +ENVO_00002146 ['Soil which has elevated concentrations of xylene.'] ['xylene contaminated soil'] +ENVO_00002875 ['Soil which has elevated concentrations of oil.'] ['oil contaminated soil'] +ENVO_00005775 ['Soil which has elevated concentrations of sodium chloride.'] ['salt contaminated soil'] ['salty soil'] +ENVO_06105276 ['Clay loam which has a high proportion of sand in its composition.'] ['Some authorities consider sandy clay loam to be a soil composed of 45-80% sand, 0-28% silt, and 20-35% clay.'] ['sandy clay loam'] +ENVO_06105278 ['Clay loam which has a high proportion of silt in its composition.'] ['Some authorities consider silty clay loam to be a soil composed of 0-20% of sand, 40-73 of silt and 27-40% of clay.'] ['silty clay loam'] +ENVO_01001557 ['Ice which has formed as the result of freezing of water which was part of a water body.'] ['In the United States, NOAA considers ice formed from the freezing of the waters of the Great Lakes as being the same as sea ice. This class attempts to provide a distinction for clarity.'] ['water-body-derived ice'] +ENVO_01000847 ['A type of water ice that forms on dead wood with the assistance of the fungus Exidiopsis effusa and takes the shape of fine, silky hair.'] ['frost beard', 'ice wool'] ['hair ice'] ['Add quality like filamentous from PATO'] +ENVO_01001513 ['Water ice which has formed in a mass of permafrost.'] ['permafrost congelation ice'] +ENVO_03000063 ['Water ice which is formed from freezing water and is suspended in a water body.'] ['sea ice types include frazil, grease ice, slush, and shuga. These new ice classes refer to both marine water and fresh water ice. If using this term for annotation, use it in conjunction with another envo term to express whether the ice is in a marine, freshwater, or other system.'] ['new ice'] ['Currently the new ice classes are not specific to sea water as they may form in non marine systems, but it would be good to confirm this especially for frazil ice.'] +ENVO_03000004 ['Any water ice that is part of a glacier.'] ['glacial ice'] ['It is suggested that users complement this term with ice terms that are more descriptive of the ice itself, rather than its location/parthood.'] +ENVO_03000025 ['Water ice which contains material liberated during an erosion process.'] ['erosionally enriched ice'] +ENVO_03000007 ['Water ice containing little to no air bubbles resulting in a reduction of internal light scattering and, given sufficient volume, a blue appearance.'] "[""The blue 'appearance' is to be understood as that within the visual range of humans.""]" ['blue ice'] +ENVO_00002053 ['A sedimentary rock which is composed primarily of calcium carbonate in the form of calcite or aragnoite.'] ['limestone'] "['An interesting reasoning error was generated when this class had ""composed primariy of some CHEBI:calcium carbonate"". As that was a CHEBI:mineral, and minerals are disjoint from ENVO:rock, it led to an unsatisfiable class. The current axiom works around this, but this is requires some sort of geological convention to diffferentiate between masses of minerals and rocks that are composed primarily of minerals.']" +ENVO_01000271 ['Clastic sedimentary rocks are sedimentary rocks that are composed of silicate minerals and rock fragments that were transported by moving fluids. Clastic rocks are composed largely of quartz, feldspar, rock (lithic) fragments, clay minerals, and mica; numerous other minerals may be present as accessories and may be important locally.'] ['clastic sedimentary rock'] +ENVO_02000091 ['A combustible black or brownish-black sedimentary rock usually occurring in rock strata in layers or veins called coal beds or coal seams.'] ['coal'] +ENVO_00010623 ['A sedimentary carbonate rock and a mineral, both composed of calcium magnesium carbonate CaMg(CO3)2 found in crystals.'] ['dolomite'] +ENVO_01000962 ['A sedimentary rock which is primarily composed of the fossilized, siliceous remains of diatoms mixed with varying amounts of other clays and minerals.'] ['kieselguhr', 'kieselgur'] ['This material is easily crumbled into a fine white to off-white powder. The powder has a particle size ranging from less than 3 micrometres to more than 1 millimetre, but typically 10 to 200 micrometres. The diatoms in each deposit contain different amounts of silica, depending on the age of the deposit. The species of diatom may differ among deposits. The species of diatom is dependent upon the age and paleo-environment of the deposit. In turn, the shape of a diatom is determined by its species. The typical chemical composition of oven-dried diatomaceous earth is 80 to 90% silica, with 2 to 4% alumina (attributed mostly to clay minerals) and 0.5 to 2% iron oxide.'] ['diatomite'] ['diatomaceous earth', 'D.E.'] +ENVO_03600064 ['A sedimentary rock which is made of carbonate mud whose formation is mediated by microbes in the benthic zone.'] ['microbialite'] +ENVO_00002014 ['An igneous rock that results from the crystallization of a magma below the surface of the Earth.'] ['plutonic rock'] ['intrusive rock'] +ENVO_01000236 ['Basalt is a volcanic rock which is formed by the rapid cooling of basaltic lava.'] ['basalt'] +ENVO_01000356 ['A portion of granite is a portion of igneous rock which is intrusive, felsic, granular, and phaneritic.'] ['Requested in issue 45. Some relations to PATO and SWEET classes suggested.'] ['granite'] +ENVO_01000441 ['Andesite is an extrusive igneous, volcanic rock, of intermediate composition, with aphanitic to porphyritic texture.'] ['In a general sense, it is the intermediate type between basalt and dacite, and ranges from 57 to 63 percent silicon dioxide as illustrated in TAS diagrams. The mineral assemblage is typically dominated by plagioclase plus pyroxene and/or hornblende. Magnetite, zircon, apatite, ilmenite, biotite, and garnet are common accessory minerals. Alkali feldspar may be present in minor amounts.'] ['andesite'] +ENVO_01000442 ['Dacite is an igneous, volcanic rock. It has an aphanitic to porphyritic texture and is intermediate in composition between andesite and rhyolite. Dacite consists mostly of plagioclase feldspar with biotite, hornblende, and pyroxene (augite and/or enstatite). It has quartz as rounded, corroded phenocrysts, or as an element of the ground-mass. The plagioclase ranges from oligoclase to andesine and labradorite. Sanidine occurs, although in small proportions, in some dacites, and when abundant gives rise to rocks that form transitions to the rhyolites.'] ['dacite'] +ENVO_01000274 ['Slate is a metamorphic rock which is fine-grained, foliated, homogeneous, Slates are derived from clastic sedimentary rocks.'] ['slate'] +ENVO_02000095 ['Ore which contains uranium.'] ['The primary uranium ore mineral is uraninite'] ['uranium ore'] +ENVO_01000681 ['A mineral material composed primarily of sodium chloride.'] ['sodium chloride salt'] ['This class is for material primarily composed of sodium chloride. For other pure chemical salts, consider a CHEBI class. Request new ENVO terms for environmental samples of other chemical salts.'] ['salt'] +ENVO_01001288 ['Dust which is primarily composed of kaolinite particles.'] ['kaolinite dust'] ['kaolin dust'] +ENVO_02000107 ['Dust that comes from grain and all the other substances associated with its cultivation & harvesting.'] ['grain dust'] +ENVO_01001186 ['Volcanic ash which has increased levels of molecules or ions capable of donating a hydron (proton or hydrogen ion) to other chemical entities, or, alternatively, capable of forming covalent bonds with other chemicals via the acceptance of an electron pair, resulting in a bulk pH measurement of less than 7.'] ['acidic volcanic ash'] +ENVO_02000128 ['A very fine, powdery material composed mostly of silica made from the burning of finely ground coal in a boiler.'] ['fly ash'] +ENVO_02000129 ['a coarse, angular ash particle that is too large to be carried up into the smoke stacks so it forms in the bottom of the coal furnace.'] ['bottom ash'] +ENVO_02000130 ['molten bottom ash from slag tap and cyclone type furnaces that turns into pellets that have a smooth glassy appearance after it is cooled with water.'] ['boiler slag'] +ENVO_02000131 ['a material leftover from the process of reducing sulfur dioxide emissions from a coal-fired boiler that can be a wet sludge consisting of calcium sulfite or calcium sulfate or a dry powered material that is a mixture of sulfites and sulfates.'] ['flue gas desulfurization material'] +ENVO_01000415 ['A portion of fine respirable suspended particulate matter is a form of particulate matter composed primarily of solid particles each with a diameter of 2.5 micrometers or less.'] ['PM2.5'] ['fine respirable suspended particulate matter'] +ENVO_01000482 ['Soda-lime glass is a silica-based glass which is composed of approximately 75% silicon dioxide, with sodium oxide and calcium oxide consituting most of its remaining composition.'] ['soda-lime-silica glass'] ['This type of glass constitutes 90% of manufactured glass.'] ['soda-lime glass'] ['glass'] +ENVO_01000485 ['Quartz glass is a glass which is composed of silica in amorphous (non-crystalline) form.'] ['fused quartz', 'fused silica'] "['This is ""pure"" silica glass. As an ENVO:""environmental material"" this class assumes that there remains some possibility that \'contaminants\' being present.']" ['quartz glass'] +ENVO_03520007 ['A water ice crystal which is constituted by water molecules aligned in a hexagonal array.'] ['snow crystal'] ['snowflake'] +ENVO_01001883 ['A water ice crystal which is a part of a deposit of hoarfrost and which only grows by desublimation.'] ['hoar frost crystal'] ['hoar crystal'] ['white frost crystal'] +ENVO_01000851 ['A clathrate material in which a large amount of methane is trapped within a crystal structure of water, forming a solid similar to ice.'] ['fire ice', 'gas hydrate', 'hydromethane', 'methane hydrate', 'methane ice', 'natural gas hydrate'] ['methane clathrate'] +ENVO_01001236 ['Planktonic kerogen which has high concentrations of sulfur compounds.'] ['sulfrous kerogen'] +ENVO_01001846 ['Hoar which is usually cup-shaped and facetted and which forms within dry, low-density snow beneath the snow surface.'] ['Depth hoar is associated with very fast crystal growth under large temperature gradients. Sometimes a layer of depth hoar forms just above, and may assist in identifying the summer surface. The low density and low strength of depth hoar can make it difficult to retrieve unbroken core sections during coring, and can complicate estimates of accumulation by microwave remote sensing. Layers of depth hoar also increase the likelihood of avalanching. This is one way in which firn formation may begin. Depth hoar is similar in physical origin to crevasse hoar.'] ['depth hoar'] +ENVO_01001882 ['Hoar which a) forms on surfaces, b) occurs when the temperature of the surface is colder than the air above and colder than the frost point of that air.'] ['When buried by snowfall, surface hoar may be considered depth hoar. The crystals formed by surface hoar are usually leaf-, fern- or plate-shaped and facetted. Two types of surface hoar are the fernlike ice crystals deposited directly on a snow surface and the hoarfrost that has grown primarily in two dimensions, as on a window or other smooth surface.'] ['surface hoar'] +ENVO_03605001 ['Periphyton colonizing rock substrata'] ['epilithon'] +ENVO_03605002 ['Periphyton colonizing silt substrata'] ['epipelon'] +ENVO_03605003 ['Periphyton colonizing surface of aquatic plants'] ['epiphyton'] +ENVO_03605004 ['Periphyton colonizing sand substrata'] ['epipsammon'] +ENVO_03605005 ['Periphyton colonizing woody substrata'] ['epixylon'] +ENVO_00002147 ['Coal mine lake sediment is lake sediment which covers the bottom of a coal mine lake.'] ['coal mine lake sediment'] +ENVO_00002209 ['Saline lake sediment is sediment which covers the bottom of a saline lake.'] ['saline lake sediment'] ['soda lake sediment'] +ENVO_01000135 ['Sediment hosting and characterised by active nitrate reducing microbial communities.'] ['nitrate-reducing sediment'] +ENVO_01000151 ['Sediment hosting and characterised by active manganese reducing microbial communities.'] ['manganese-reducing sediment'] +ENVO_01000152 ['Sediment hosting and characterised by active iron reducing microbial communities.'] ['iron-reducing sediment'] +ENVO_01000153 ['Sediment hosting and characterised by active sulphate reducing microbial communities.'] ['sulphate-reducing sediment'] +ENVO_01000154 ['Sediment hosting and characterised by active carbon dioxide reducing microbial communities.'] ['carbon dioxide-reducing sediment'] +ENVO_00002113 ['Sediment that accumulates in the flat or very gently sloping areas of the deep ocean basin floor. The three main types of deep marine sediment, also known as pelagic sediment, are siliceous oozes, calcareous oozes, and red clays.'] ['deep marine sediments'] ['deep marine sediment'] ['pelagic sediment {alternative name}'] +ENVO_03000034 ['Marine sediment soured from either terrestrial systems, marine organisms, seawater and or cosmogeneous sources, which is transported through the marine water column, and accumulates within shallow regions of the oceanic basin close to continents, such as the continental shelf, or continental slope.'] ['shallow marine sediments'] ['shallow marine sediment'] ['In this definition we refer to sedimentation processes that occured above the shelf, however this should be relaxed to include the continental shelf and slope.', 'output of sedimentation process which occured in neritic zone biome'] ['neritic marine sediment'] +ENVO_00002202 ['Chemically-enriched sediment which has increased levels of organic compounds.'] ['organically enriched sediment'] +ENVO_00002203 ['Chemically-enriched sediment which has increased levels of inorganic compounds.'] ['inorganically enriched sediment'] +ENVO_03600001 ['Sediment which contains some chemical contaminant.'] ['chemically contaminated sediment'] "[""See https://github.com/EnvironmentOntology/envo/issues/1102 for a possible design pattern.\n\nUses undesirability standard, compared to polluted river's ecological impact standard. What is the relation to ENVO:00002114 'chemically enriched sediment'? Does 'element' in the definition refer to something found in the periosic table (like selenium) or the member of some set, aka an entity?""]" +ENVO_02000044 ['Siliceous ooze is a marine sediment composed of the debris of plankton with silica shells, such as diatoms and radiolaria. This ooze is limited to areas with high biological productivity, such as the polar oceans, and upwelling zones near the equator. The least common type of sediment, it covers only 15% of the ocean floor. It accumulates at a slower rate than calcareous ooze: 0.2-1 cm / 1000 yr.'] ['siliceous ooze'] +ENVO_02000045 "['Red clay, also known as pelagic clay, accumulates in the deepest and most remote areas of the ocean. Containing less than 30% biogenic material, its composition is a varied mix of very fine quartz and clay minerals, authigenic deposits precipitated directly from seawater, and micrometeorites. Though called ""red"" because it sometimes takes the color of oxidized iron minerals, it is usually brownish in color. Its ultimate origin is uncertain, but red clay seems to be mostly derived from distant rivers, and windblown dust. Covering 38% of the ocean floor, it accumulates more slowly than any other sediment type, at only 0.1-0.5 cm / 1000 yr.']" ['red clay'] +ENVO_02000046 "[""Calcareous ooze is a marine sediment composed primarily of the shells--also known as tests--of foraminifera, coccolithophores, and pteropods. This is the most common pelagic sediment by area, covering 48% of the world ocean's floor. This type of ooze is limited to depths above the Carbonate Compensation Depth at time of burial. It accumulates more rapidly than any other pelagic sediment type, with a rate that varies from 0.3 - 5 cm / 1000 yr.""]" ['calcareous ooze'] +ENVO_01000112 ['Polymetallic nodules, also called manganese nodules, are rock concretions on the sea bottom formed of concentric layers of iron and manganese hydroxides around a core. Nodules vary in size from tiny particles visible only under a microscope to large pellets more than 20 centimetres (8 in) across. However, most nodules are between 5 and 10 cm in diameter.'] ['manganese nodule'] ['polymetallic nodule'] +ENVO_03501252 ['Poultry manure made of chicken feces.'] ['chicken manure'] +ENVO_01000460 ['Asphalt also known as bitumen is a sticky, black, and highly viscous liquid or semi-solid form of petroleum.'] ['asphaltum', 'bitumen', 'crude bitumen'] ['This class refers to naturally-occuring asphalt or bitumen.'] ['asphalt'] ['pitch', 'tar'] +ENVO_03510006 ['A liquid fuel used in diesel engines, whose fuel ignition takes place, without any spark, as a result of compression of the inlet air mixture and then injection of fuel.'] ['diesel fuel'] ['petroleum distillate fuel oil'] +ENVO_03510007 ['A clear petroleum-derived flammable liquid which is used as fuel in most spark-ignited internal combustion engines.'] ['gas', 'petrol'] ['Gasoline consists mostly of organic compounds obtained by the fractional distillation of petroleum, enhanced with a variety of additives.'] ['gasoline'] +ENVO_01000551 ['A fuel oil which is 1) composed primarily of alkanes having between 5-15 carbon atoms with the general formula CnH2n+2, 2) is generally odorless or has only a slight odor, 3) produces only small amounts of soot relative to other fuel oils, 4) is highly refined.'] ['liquid paraffin'] ['paraffin oil'] ['paraffin'] +ENVO_01001608 ['A fuel oil which 1) is derived from petroleum oil, 2) has a strong odor, 3) produces large quantities of soot relative to other fuel oils, 4) is less refined than fuel oils such as paraffin.'] ['kerosine oil', 'liquid kerosene'] ['For speakers of British English, kerosene is often referred to as paraffin.'] ['kerosene oil'] ['kerosene', 'kerosine'] +ENVO_01000555 ['Compressed natural gas is a natural gas stored at high pressures, typically 20–25 Megapascals.'] ['compressed natural gas'] +ENVO_01000559 ['Compressed biogas is biogas stored at increased pressures.'] ['This is distinct from compressed natural gas, which refers to the compressed form of a fossil fuel.'] ['compressed biogas'] +ENVO_01000842 ['A fog which is intermixed with smoke or other combustion products and their derivatives.'] ['smog'] +ENVO_01001258 ['A fog which is composed of liquid aerosols and gases derived from volcanic gas emissions (primarily sulfur oxides), formed when sulfur-bearing gases react with sunlight, oxygen, and moisture in an atmosphere.'] "['""Vog and smog are different. Vog is formed when sulfur oxides emitted by a volcano react with moisture to form an aerosol. The aerosol scatters light, thus making the vog visible. Smog is formed largely from the incomplete combustion of fuel, reacting with nitrogen oxides and ozone produced from carbon monoxide by reactions with sunlight. The result is also a visible aerosol.""']" ['vog'] +ENVO_03000137 ['A fog the droplets of which freeze upon contact with exposed objects, forming a coating of rime or glaze.'] ['Freezing fog forms when the air temperature is below freezing and the water droplets in the fog become supercooled.'] ['freezing fog'] +ENVO_01000676 ['Contaminated air is air which has sufficient concentrations of environmental pollutants such that it may adversely affect a given ecosystem.'] ['contaminated air'] +ENVO_01000828 ['Air which has increased levels of water vapour.'] ['humid air'] +ENVO_01000268 ['Atmospheric water vapour is water vapour that is part of an atmosphere.'] ['atmospheric water vapor'] ['atmospheric water vapour'] +ENVO_01000770 ['A volume of carbon dioxide gas emitted by a carbon dioxide emission process.'] ['This is a working definition for #280. Which processes will ultimately be included in the axioms is still open.'] ['carbon dioxide emission'] +ENVO_01000790 ['A flame which is produced by the combustion of hydrocarbon fuel.'] ['hydrocarbon flame'] +ENVO_02000115 ['Respirable vapor of vanadium.'] ['vanadium fume'] +ENVO_00002010 ['Water which contains a significant concentration of dissolved salts.'] ['salt water'] ['The threshold salt concentration for classifying water as saline varies, but typically begins at about 1,000 to 3,000 parts salt per million parts water or 0.1–0.3% salt by weight.'] ['saline water'] +ENVO_00002011 ['Water which has a low concentration of dissolved solutes, particularly that of sodium chloride.'] ['freshwater'] ['The lower bound of solute concentration required for water to be considered freshwater is variable, but is always less than that of seawater, and often cited as less than 1 gram of solutes per 1 litre of water.'] ['fresh water'] ['sweet water'] +ENVO_01000722 ['Meltwater is the water released by the melting of snow or ice, including glacial ice, tabular icebergs and ice shelves over oceans.'] ['meltwater'] +ENVO_00002042 ['Water that is found on the surface of an astronomical object.'] ['surface water'] +ENVO_01000357 ['A portion of alkaline water is a portion of water with a pH greater than 7.'] ['Here, we commit to a threshold of pH as this is almost universally accepted.'] ['alkaline water'] +ENVO_01000358 ['A portion of acidic water is a portion of water with a pH less than 7.'] ['acidic water'] +ENVO_00002141 ['The liquid produced when water percolates through any permeable material. It can contain either dissolved or suspended material, or usually both.'] ['leachate'] +ENVO_00002223 ['Water which has very low concentrations of nutrients.'] ['oligotrophic water'] +ENVO_00002224 ['Water with a high nutrient level.'] ['eutrophic water'] +ENVO_00002225 ['Water with a nutrient level intermediate between eutrophic and oligotrophic.'] ['mesotrophic water'] +ENVO_00005791 ['Sterile water is water which does not contain lliving organisms.'] ['sterile water'] +ENVO_00005792 ['Water which has physicochemical properties determined by processes which occur beneath the planetary crust.'] "['This class references any water that\'s under a planetary surface. For water that is in an aquifer, see ""groundwater"" (ENVO:01001004). Previously, this class included both.']" ['underground water'] ['subterranean water'] +ENVO_01000173 ['Water which lacks dissolved oxygen.'] ['anaerobic water'] ['anoxic water'] ['reducing water'] +ENVO_03605006 ['Water which is part of a stream.'] ['stream water'] +ENVO_01000872 ['Ballast water is water contained in the ballast tanks of sea-going vessels.'] ['This definition could be improved, as ballast water is often used in more general ways, beyond the water contained in a ballast tank at any given time. For example, water which has just been released from a ballast tank is often still refered to as ballast water.'] ['ballast water'] +ENVO_01000940 ['Water which is partially contained within a fissure or a geological fracture.'] ['fracture water'] "[""While containment is often enough to classify this subtype of water, it is expected that the water's composition is altered by contact with the solid material bounding the fissure's site.""]" ['fissure water'] ['The axiomatisation should be more tuned to the site within the fissure.'] +ENVO_01001063 ['Water which has an appreciable concentration of dissolved oxygen.'] ['The threshold dissolved oxygen concentration past which water is considered oxic is variable. Typically, this is understood as the concentration at and beyond which organisms inhabiting that water can sustain aerobic metabolism and good health. For most systems, this is above 80% oxygen saturation. Input is welcome here https://github.com/EnvironmentOntology/envo/issues/536'] ['oxic water'] +ENVO_01001064 ['Water which has low levels of dissolved oxygen.'] ['As with oxic and anoxic water, the thresholds for hypoxia are variable. Typically, a hypoxic state is asserted when dissolved oxygen levels decrease to a level where they have detrimental effects on aerobic aquatic organisms, typically below 30% oxygen saturation.'] ['hypoxic water'] +ENVO_01001267 ['Water which accumulates on a solid surface during precipitation events and snow/ice melt.'] ['storm water'] "['""Stormwater can soak into the soil (infiltrate), be held on the surface and evaporate, or runoff and end up in nearby streams, rivers, or other water bodies (surface water).""']" ['stormwater'] +ENVO_03501370 ['A liquid water which has no current or flow and is susceptible to contamination by pathogens or pathogenic vectors.'] ['stagnant water'] ['wet'] +ENVO_03600002 ['Liquid water which is a participant in a water cooling process.'] ['Cooling water is commonly used for cooling automobile internal combustion engines and power stations.'] ['cooling water'] +ENVO_03600009 ['Liquid water which occurs naturally within the pores of rocks and sediments.'] ['interstitial water'] +ENVO_03600042 ['Liquid water which is either part of or was removed from a marine lake.'] ['marine lake water'] +ENVO_03600065 ['Water which comes from a spring.'] ['spring water'] +ENVO_04000007 ['Water which is part of a lake.'] ['lake water'] +ENVO_06105211 ['Liquid water which 1) flows over land and 2) is not absorbed or retained by the materials if flows over or through.'] ['overland flow', 'surface runoff'] ['Runoff often gathers debris and solutes from the materials it flows over or through, and often flows into a water body.'] ['runoff'] +ENVO_06105238 ['Liquid water which is present in soils as discontinuous volumnes of water in contact with solid and gaseous components of the soil.'] ['residual water in soil'] +ENVO_06105268 ['Waste water which was converted into an effluent that can be either returned to the water cycle with minimal environmental issues or reused.'] ['treated wastewater'] +ENVO_06105269 ['Saline water from which minerals have been removed to produce fresh water suitable for human consumption or irrigation.'] ['desalinated water'] +ENVO_01001514 ['Freshwater ice which forms downward from the surface of a freshwater water body and is transparent due to a reduced number of air bubbles trapped in its mass.'] ['black ice'] ['congelation ice in a fresh water body'] +ENVO_01001516 ['Freshwater congelation ice which has formed on a solid substrate in an ice cave.'] ['ice cave congelation ice'] +FOODON_00001015 ['This class includes food products which are derived from or produced by a plant.'] ['plant food product'] +FOODON_00004242 ['A food product deriving from one or more animals.'] ['animal food product'] +FOODON_00001184 ['This food product type includes food products which are derived from a large, diverse group of photosynthetic organisms.'] ['algal food product'] +FOODON_00001079 ['A food preserved by soaking and storing it in vinegar or brine.'] ['pickled'] "[""SIREN DB annotation:\n* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151)\n* formed as a result of 'pickling process' (http://purl.obolibrary.org/obo/FOODON_03460190)""]" ['food (pickled)'] +FOODON_00001133 ['A relish, sauce, or seasoning added to food to impart a particular flavour or to complement the dish.'] ['condiment'] ['condiment food product'] +FOODON_03420228 ['A physical-chemical component separated from the food source or its parts by extraction, centrifugation, filtration, heat processing, expressing or a similar process. The separated component may be converted through further processing. If this is done, the final substance is indexed. A water-extracted component may remain in aqueous dispersion. The extract, concentrate or isolate is indexed in preference to the anatomic part from which it is derived. For example, peanut oil is indexed under *PEANUT* combined wih *FAT OR OIL* rather than with *SEED OR KERNEL*. On the other hand, fruit and vegetable juices can be indexed under *FRUIT JUICE OR NECTAR* or *VEGETABLE JUICE* (A. PRODUCT TYPE); therefore the anatomic part of the plant should be indexed.'] "[""Damion Dooley's note: Items in this branch will be merged into foodon food product branch.""]" ['extract, concentrate or isolate of plant or animal'] +FOODON_00001149 ['Food items that are rich in sugar, any one or type of which is called a confection. Modern usage may include substances rich in artificial sweeteners as well.'] ['confectionery food product'] +FOODON_03301977 ['A liquid prepared for consumption, or a product that can be combined with water or milk to make one.'] ['beverage food product'] +FOODON_00002175 ['A prepared hen egg product is a product predominantly made of hen egg that has been cooked and may only require defrosting or reheating for consumption.'] ['prepared hen egg product'] +FOODON_03430130 "[""A state of matter between a solid and a gas, in which a substance has the capacity to flow and conforms to the shape of the container. Liquids range from water to honey, corresponding to a range in viscosity (or apparent viscosity) from 1 to 500 centipoise (viscosity is a measure of a liquid's resistance to flow). Products that are pourable but have a higher viscosity are *SEMILIQUID*.""]" "[""SIREN DB annotation:\n* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130)\n ""]" ['food (liquid)'] +FOODON_03401270 ['Food and Drugs, title 21, Code of Federal Regulations. Original food classification in LanguaL.'] ['LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term.'] ['U.S. code of federal regulations, title 21 food product type'] +FOODON_03400643 "[""Codex Alimentarius, Volume 2 - 1993, Section 2: Pesticide Residues in Food.\n\nThe Codex Classification of food and animal feed commodities moving in trade and the description of the various items and groups of food and animal feedstuffs included in the present document have been developed by the Codex Committee on Pesticide Residues. It was first adopted by the 18th Session of the Codex Alimentarius Commission, (1989).\n\nThe Codex Classification includes food commodities and animal feedstuffs for which Codex maximum residue limits will not necessarily be established. The Classification is intended to be as complete a listing of food commodities in trade as possible, classified into groups on the basis of the commodity's similar potential for pesticide residues.\n\nThe Classification may also be appropriate for other purposes such as setting maximum levels for other types of residues or for other contaminants in food. The Codex Classification should be consulted in order to obtain a precise description of the food or animal feed commodities and, especially, in cases where Codex maximum residue limits have been set for groups of food and groups of animal feedstuffs. The Codex Classification is intended to promote harmonization of the terms used to describe commodities which are subject to maximum residue limits and of the approach to grouping commodities with similar potential for residue for which a common group maximum residue limit can be set.""]" ['LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term.'] ['Codex Alimentarius classification of food and feed commodities'] +FOODON_03400874 ['The Global System 1 (GS1) Global Product Classification (GPC) is a system that gives buyers and sellers a common language for grouping products in the same way, everywhere in the world.$br/$\nThe GS1 GPC classification in facet A is currently updated based on June 2017 release of GS1 GPC Standard for Food/Beverage/Tobacco, except for codes pertaining to tobacco. See the GS1 site for details [https://www.gs1.org/standards/gpc].'] ['GS1 Global Product Classification (GPC)'] +ENVO_00002145 ['Soil which has elevated concentrations of chromate.'] ['chromate contaminated soil'] +ENVO_00002200 ['Water ice which has formed by the freezing of sea water.'] ['In the United States, NOAA sea ice operations does not include superstructure icing as being sea ice. In sea ice operations however, sea ice is any form of ice found at sea which has originated from the freezing of sea water. It presents the main kind of floating ice encountered at sea. Except where it forms ridges, sea ice is up to a few metres thick, in which respect it differs from shelf ice. Sea ice may be discontinuous pieces (ice floes) moved on the ocean surface by wind and currents (pack ice), or a motionless sheet attached to the coast (land-fast ice). In brief, it forms first as lolly ice (frazil crystals), thickens into sludge, and coagulates into sheet ice, pancake ice, or into floes of various shapes and sizes. Thereafter, sea ice may develop into pack ice and/or become a form of pressure ice. Sea ice less than one year old is called first-year ice. Perennial ice is sea ice that survives at least one summer. It may be subdivided into second-year ice and multi-year ice, where multiyear ice has survived at least two summers.'] ['sea ice'] ['Parse comment from GCW and new subclases where appropriate.'] +ENVO_01001523 ['Small, needle-like (spicules), plate-like, or discoid crystals derived from nearly pure fresh water, suspended in a water body.'] ['frazil crystals', 'needle ice'] ['Typically 3 to 4 millimeters in diameter. These may form in both marine water and fresh water. They represent the first stages of sea ice growth; they merge under calm conditions to form thin sheets of ice on the surface (frazil ice), and consist of nearly pure fresh water. In fresh water, they form in supercooled water that is too turbulent to permit coagulation into sheet ice. This is most common in swiftly flowing streams. They may accumulate as anchor ice on submerged objects obstructing the water flow.'] ['frazil'] ['Needs to have axioms added pertaining to the semantics of colloids and suspensions once they have been resolved see: https://github.com/pato-ontology/pato/issues/91#issuecomment-290711238\n\nCurrently the new ice classes are not specific to sea water as they may form in non marine systems, but it would be good to confirm this especially for frazil ice.'] +ENVO_03000046 ['New ice which is composed frazil which has congealed into a thin sheet.'] ['Typically 3 to 4 millimeters in diameter. These new ice classes refer to both marine water and fresh water ice. If using this term for annotation, use it in conjunction with another envo term to express whether the ice is in a marine, freshwater, or other system.'] ['frazil ice'] ['Needs to have axioms added pertaining to the semantics of colloids and suspensions once they have been resolved see: https://github.com/pato-ontology/pato/issues/91#issuecomment-290711238\n\nCurrently the new ice classes are not specific to sea water as they may form in non marine systems, but it would be good to confirm this especially for frazil ice.'] +ENVO_03000075 ['New ice, which is spongy, lumpy and opaque, and forms from water which freezes in an agitated water body.'] ['These new ice classes refer to both marine water and fresh water ice. If using this term for annotation, use it in conjunction with another envo term to express whether the ice is in a marine, freshwater, or other system.'] ['shuga'] +ENVO_03000005 ['Glacial ice which contains material liberated during a glacial erosion process.'] ['erosionally enriched glacial ice'] +ENVO_00002054 ['Limestone which is soft, white, and porous.'] ['chalk'] +ENVO_00003982 ['Limestone which is deposited from the water of mineral springs or streams saturated with calcium carbonate.'] ['travertine'] +ENVO_01000273 ['Lime mudstone is a limestone which is primarily composed of either clay-size or both silt-size and clay-size detrital (transported) carbonate grains.'] ['calcilutite', 'cementstone'] "['https://en.wikipedia.org/wiki/ The terminology of ""mudstone"" is not to be confused with the Dunham classification scheme for limestones. In Dunham\'s classification, a mudstone is any limestone containing less than ten percent carbonate grains. Note, a siliciclastic mudstone does not deal with carbonate grains. Friedman, Sanders, and Kopaska-Merkel (1992) suggest the use of ""lime mudstone"" to avoid confusion with siliciclastic rocks.']" ['lime mudstone'] +ENVO_00002055 ['A sedimentary rock composed mainly of sand-size mineral or rock grains.'] ['sandstone'] +ENVO_00002056 ['A fine-grained sedimentary rock whose original constituents were clays or muds. It is characterized by thin laminae breaking with an irregular curving fracture, often splintery and usually parallel to the often-indistinguishable bedding plane.'] ['shale'] +ENVO_01000269 ['A sedimentary rock which is composed mainly of silt. This rock has a grainsize in the silt range, finer than sandstone and coarser than claystones.'] ['siltstone'] +ENVO_01000270 ['A clastic sedimentary rock which is composed primarily of clay sized particles.'] ['claystone'] +ENVO_01000272 ['A mudstone is a clastic sedimentary rock which contains a mixture of at least one third of silt- and one third of clay-sized particles.'] "['There is debate on the usage of mudstone and mudrock, and some ambiguity is to be expected. https://en.wikipedia.org/wiki/ The terminology of ""mudstone"" is not to be confused with the Dunham classification scheme for limestones. In Dunham\'s classification, a mudstone is any limestone containing less than ten percent carbonate grains. Note, a siliciclastic mudstone does not deal with carbonate grains. Friedman, Sanders, and Kopaska-Merkel (1992) suggest the use of ""lime mudstone"" to avoid confusion with siliciclastic rocks.']" ['mudstone'] +ENVO_2000008 ['A soft, brown, combustible, sedimentary rock formed from naturally compressed peat.'] ['brown coal'] ['It is considered the lowest rank of coal due to its relatively low heat content. It has a carbon content around 60–70 percent.'] ['lignite'] +ENVO_2000010 ['a relatively soft coal containing a tarlike substance called bitumen or asphalt. It is of higher quality than lignite coal but of poorer quality than anthracite. It is an organic sedimentary rock formed by diagenetic and sub metamorphic compression of peat bog material.'] ['black coal'] ['bitumous coal'] +ENVO_2000011 ['A hard, compact variety of coal that has a submetallic luster. It has the highest carbon content, the fewest impurities, and the highest energy density of all types of coal and is the highest ranking of coal.'] ['hard coal'] ['anthracite'] +ENVO_2000044 ['Coal heated in the absence of air.'] ['coke'] +ENVO_01000416 ['A portion of fine respirable suspended particulate matter is a form of particulate matter composed primarily of solid particles each with a diameter of 100 nanometers or less.'] ['Regulations do not exist for this size class of ambient air pollution particles, which are far smaller than the regulated PM10 and PM2.5 particle classes and are believed to have several more aggressive health implications than those classes of larger particulates.'] ['ultrafine respirable suspended particulate matter'] +ENVO_01000483 ['Flat glass is a soda-lime glass which is composed of approximately 73% silicon dioxide (silica), 14% sodium oxide, 9% calcium oxide, 4% magnesium oxide, 0.15% aluminium oxide, 0.03% potassium oxide, 0.02% titanum dioxide, and 0.01% iron III oxide.'] ['plate glass', 'sheet glass'] ['Most flat glass is soda-lime glass produced by the float glass process. It is more water soluble than container glass.'] ['flat glass'] +ENVO_01000484 ['Container glass is a soda-lime glass which is composed of approximately 74% silicon dioxide (silica), 13% sodium oxide, 10.5% calcium oxide, 1.3% aluminium oxide, 0.3% potassium oxide, 0.2% sulphur trioxide, 0.2% magnesium oxide, 0.04% iron III oxide, and 0.01% titanum dioxide.'] ['Container glass is less water soluble than flat glass.'] ['container glass'] +ENVO_00002115 ['Organically enriched sediment which has increased levels of petroleum.'] ['petroleum enriched sediment'] +ENVO_00002180 ['Organically enriched sediment which has increased levels of naphthalene.'] ['naphthalene enriched sediment'] +ENVO_00002182 ['Organically enriched sediment which has increased levels of nitrobenzene.'] ['nitrobenzene enriched sediment'] +ENVO_00002201 ['Organically enriched sediment which has increased levels of cis-dichloroethane.'] ['cis-dichloroethane contaminated sediment'] +ENVO_01000829 ['Air which has a partial pressure of water vapour equal or near equal to its equilibrium vapor pressure at a given temperature.'] ['water-vapour-saturated air'] "['""Near equal"" is meant to reflect that there will be fluctuations around the equilibrium point.']" ['water vapour saturated air'] ['wet air'] +ENVO_00002149 ['Water which has physicochemical properties that have been determined by the processes occuring in a sea or ocean.'] ['ocean water', 'seawater'] ['This definition refers to water that is actually in a sea or ocean. This water may have a wide range of salinity levels.'] ['sea water'] ['When we have more classes representing the various processes which make seawater seawater, we can further axiomatise this class.'] +ENVO_00002019 ['Water which has a higher salinity than fresh water but a lower salinity than marine water.'] ['brackish water'] +ENVO_00002012 ['Water which contains a highly increased concentration of dissolved salts, surpassing the average salinity of seawater.'] ['The average salinity of sea water is assumed to be around 35,000 ppm, equivalent to 35 grams of salt per one liter (or kilogram) of water.'] ['hypersaline water'] ['We make no commitment to a particular threshold; this should be described on the data/information layer according to the norms of a discipline, accepted standard, or similar reference.'] +ENVO_01001037 ['Water which contains a slightly increased concentration of dissolved salts, relative to their concentration in freshwater.'] ['slightly salty water'] ['The United States Geological Survey classifies slightly saline water as having around 1,000 to 3,000 ppm (0.1–0.3%) of dissolved salts.'] ['slightly saline water'] +ENVO_01001038 ['Water which contains a moderately increased concentration of dissolved salts, relative to their concentration in freshwater.'] ['moderately salty water'] ['The United States Geological Survey classifies moderately saline water as having around 3,000 to 10,000 ppm (0.3–1%) of dissolved salts.'] ['moderately saline water'] +ENVO_01001039 ['Water which contains a highly increased concentration of dissolved salts, relative to their concentration in freshwater.'] ['highly salty water'] ['The United States Geological Survey classifies highly saline water as having around 10,000 to 35,000 ppm (1–3.5%) of dissolved salts.'] ['highly saline water'] +ENVO_01001257 ['Saline water which is derived from sea water and used during the cultivation of crustaceans.'] ['saline shrimp pond water'] +ENVO_00003064 ['Drinking water is water which may be consumed by humans with no adverse effects on their health.'] ['potable water'] ['drinking water'] +ENVO_01000600 ['Rainwater is liquid water which has precipitated in the form of droplets through the condensation of atmospheric water vapour.'] ['rainwater'] +ENVO_03600081 ['Fresh water which is harvested from cloud.'] ['cloud water'] +ENVO_01000134 ['High temperature water ejected from hydrothermal vents and laden with dissolved metals and minerals as a result of percolation through crustal rocks.'] ['hydrothermal fluid'] +ENVO_01001018 ['Water which has a very high concentration of nutrients.'] ['The thresholds of eutrophy are fluid and often locally defined.'] ['hypereutrophic water'] +ENVO_01001004 ['Underground water which is located in pore spaces found in rock or unconsolidated deposits such as soil, clay, or gravel.'] ['ground water'] ['The definition of aquifer is quite permissive, referencing any water bearing rock or unconsolidated material.'] ['groundwater'] +ENVO_01001268 ['Stormwater which accumulates in an urban ecosystem.'] ['urban storm water'] "['""Stormwater can soak into the soil (infiltrate), be held on the surface and evaporate, or runoff and end up in nearby streams, rivers, or other water bodies (surface water).""']" ['urban stormwater'] +ENVO_01001270 ['Stormwater which accumulates in a rural ecosystem.'] ['rural storm water'] "['""Stormwater can soak into the soil (infiltrate), be held on the surface and evaporate, or runoff and end up in nearby streams, rivers, or other water bodies (surface water).""']" ['rural stormwater'] +FOODON_00001007 ['A processed meat food product that is made from a sausage.'] ['sausage food product'] +FOODON_00001261 ['Any plant food product which, typically, is constituted by intact parts from one or more annual plants cultivated as field and garden crops in the open and under glass, and used almost exclusively for food.'] ['vegetable food product'] +FOODON_00001142 ['A food product deriving primarily from corn (maize).'] ['maize food product'] ['maize (corn) food product'] +FOODON_00001147 ['A food product derived from or produced by a plant root.'] ['plant root food product'] +FOODON_00001242 ['A vegetable product such as leaves, flowers, seeds and roots that is rich in essential oils and aromatic principles. Used mainly a a condiment.'] ['herb and spice', 'herb or spice'] ['spice or herb'] +FOODON_00001092 ['A food product which is derived from or produced by an animal that has a vertibrae.'] ['vertebrate animal food product'] +FOODON_00001046 ['A seafood product is a vertebrate or invertibrate organism from an aquatic environment.'] ['animal seafood product'] ['Some of the subclasses are currently freshwater organisms.'] +FOODON_00001224 ['A sausage made with fresh meats, and then fully cooked.'] ['sausage (cooked)'] +FOODON_00001281 ['A food involving whipped and cooked milk, sugar and egg yolk mixtures.'] ['sweet custard'] ['custard dessert food product'] +FOODON_00002762 ['Cooked bean material is the bean material output of a cooking process applied to dry, rehydrated, or raw (fresh) beans.'] ['bean (cooked)'] +FOODON_00002643 ['A preserved food, where the moisture levels in the food product have been reduced to low levels to improve shelf life.'] ['food (dehydrated)'] +FOODON_00001290 ['A sauce for a salad.'] ['salad dressing'] +FOODON_00002664 ['A lipid food product is a food product made primarily of plant or animal fat or oil'] ['fats and oils', 'oils and fats'] ['lipid food product'] +FOODON_03420152 ['Extract, concentrate or isolate high in sugar, oligosaccharide or polysaccharide.'] ['carbohydrate extract, concentrate, or isolate'] +FOODON_00001214 ['A confection made from a concentrated solution of sugar in water, to which flavorings and colorants are added.'] ['candy food product'] +FOODON_03430109 "[""A liquid that flows very easily at room temperature. Examples are: water, apple juice, sherry, acidophilus milk, whipping cream and some heavy liqueurs. The range of low viscosity liquid spans sucrose solutions between 0 and 45% solids (viscosity range from 1 to 10 centipoise). Prefer 'solid pieces' factor term to 'small particles' if both appear in the food.""]" ['food (liquid, low viscosity)'] +FOODON_03400164 ['Milk, a product derived from milk, or a dairy product analog; includes cheese and frozen dairy desserts. [FDA CFSAN 1995]'] ['dairy product (us cfr)'] +FOODON_03400257 ['Fruits and vegetables in all forms. [FDA CFSAN 1995]'] ['fruit or vegetable product (us cfr)'] +FOODON_03400188 ['Candy or other food product made with sweeteners and frequently containing nuts, fruits, starches, flavorings and other foods (21 CFR 170.3(n)(9). [FDA CFSAN 1995]'] ['confectionery (us cfr)'] +FOODON_03400801 ['The group includes marine or freshwater fish, molluscs, crustaceans, and other fauna such as reptiles, insects or frogs not in the \x93Meats\x94 group. The group also includes seafood product analogs and seafood-based sausage or luncheon meat as well as such products as squid ink and clam juice.'] ['seafood or related product (eurofir)'] +FOODON_03400840 ['Alcoholic or non-alcoholic beverage; excludes milk and milk-based beverages.'] ['beverage (non-milk) (eurofir)'] +FOODON_03400852 ['EFG group 32, Eurocode-2 group 12.'] ['LanguaL curation note: Use for foods and ingredients that could not fit into any of the above classes.'] ['miscellaneous food product (eurofir)'] +ENVO_01001190 ['Sea ice which has a brown colouration, either due to 1) the presence of pigments which are or were contained in the members of ecological assemblages, such as algal communities, living or trapped within the ice or 2) due to the presence of trapped sediments.'] ['brownish colored sea ice'] ['brown sea ice'] +ENVO_01001512 ['Sea ice which 1) has formed on the submerged surface (i.e. the base) of an existing mass of sea ice and 2) is composed of columnar crystals due to the downward growth of the crystals into the water.'] ['Congelation ice usually forms through the fusion/coalescence of platelets into solid ice.'] ['congelation sea ice'] ['black ice'] +ENVO_03000071 ['Sea ice which has formed over a single freezing season.'] ['Sea ice develops from young ice; thickness from 0.3 to 2 meters (1 to 6.6 feet). Sea ice be subdivided into thin first-year ice (white ice), medium first-year ice, and thick first-year ice. First-year ice is distinguished from older ice primarily by having a higher salinity. Undeformed first-year ice differs from older ice in that it is smoother and lacks refrozen melt ponds. Characteristically level where undisturbed by pressure, but where ridges occur, they distinguished by being larger, more angular, and more porous than multiyear ridges.'] ['first year ice'] ['seasonal ice'] +ENVO_03000072 ['Sea ice which is thicker than first year ice, and has survived a seasonal melting process.'] ['second year ice'] +ENVO_03000073 ['Sea ice which is thicker than second year ice, and has survived more than two seasonal melting process.'] ['multiyear ice'] +ENVO_02000119 ['An organic-rich fine-grained sedimentary rock containing kerogen from which liquid hydrocarbons called shale oil can be produced.'] ['kerogen shale'] ['oil shale'] +ENVO_00002150 ['Coastal sea water is sea water that is adjacent to a coast.'] ['coastal ocean water', 'coastal oceanic water', 'coastal seawater'] "['The limits of what qualifies as ""adjacent to"" vary greatly. This should be defined on a data level and is left intentionally fuzzy here. The label is ""coastal sea water"" rather than ""coastal water"" as some large lakes are often said to have coasts.']" ['coastal sea water'] ['coastal water'] +ENVO_01000301 ['Brackish water which is part of an estuary.'] ['estuarine water'] +ENVO_00003044 ['Water saturated or nearly saturated with salt (NaCl).'] ['It is used (now less popular than historically) to preserve vegetables, fish, and meat.'] ['brine'] +FOODON_03315904 ['A food product that is highly seasoned minced meat and is encased in a skin in the shape of a cylinder.'] ['sausage'] "[""SIREN DB annotation:\n* has quality 'whole, shape achieved by forming' (http://purl.obolibrary.org/obo/FOODON_03430147)\n* derives from 'meat part of animal' (http://purl.obolibrary.org/obo/FOODON_03420103)\n* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227)\n ""]" ['sausage (whole)'] +FOODON_00001061 ['Any of certain cuts of meat taken from the sides, belly or back of a pig that may be cured and/or smoked.'] ['bacon food product'] +FOODON_00002139 ['An edible plant fat or oil product with characteristics that consumers desire such as bland flavour and odour, clear appearance, light colour, stability to oxidation and suitability for frying, and which is the result of a refining process that removes free fatty acids.'] ['plant fat or oil refined food product'] +FOODON_00003341 ['A genus of plants in the mustard family (Brassicaceae). The members of the genus are informally known as cruciferous vegetables, cabbages, or mustard plants.'] ['brassica food product'] ['bok choy vegetable food product', 'bomdong vegetable food product', 'broccolini vegetable food product', 'chinese cabbage vegetable food product', 'choy sum vegetable food product', 'collard greens vegetable food product', 'gai lan vegetable food product', 'komatsuna vegetable food product', 'mizuna vegetable food product', 'rutabaga vegetable food product', 'savoy cabbage vegetable food product', 'tatsoi vegetable food product'] ['cole crop vegetable food product', 'cruciferous vegetable food product'] +FOODON_00001057 ['A food product derived from plant fruit.'] ['plant fruit food product'] +FOODON_00001103 ['This food product type includes beverage products which are made from the fermented sap of the maguey (agave) plant.'] ['fermented agave beverage'] +FOODON_00001264 ['A one-celled fruit (pod) usually dehiscing down both sutures, and having the seed attached along a ventral suture. (Roubik 1995)'] ['legume'] ['legume food product'] ['http://purl.obolibrary.org/obo/FOODON_03411338'] +FOODON_03460263 ['A fat or oil derived from vegetable material'] ['This is a convenience class inherited from LanguaL'] ['vegetable fat or oil'] +FOODON_00001230 ['A product made from the seeds of a mustard plant (white or yellow mustard, Sinapis hirta; brown or Indian mustard, Brassica juncea; or black mustard, Brassica nigra).'] ['mustard seed food product'] +FOODON_00001006 ['A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals.'] ['mammalian meat food product'] +FOODON_00001256 ['A dairy food product has mammilian milk or a milk component as an ingredient.'] ['dairy product', 'milk product'] ['dairy food product'] +FOODON_00001248 ['A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins).'] ['fish food product'] +FOODON_00001023 ['Cream component produced by churning and containing not less than 80% milkfat.'] ['mammalian milk butter'] +FOODON_00001014 ['A dairy product produced by bacterial fermentation of milk.'] ['yoghourt', 'yoghurt', 'yougert'] ['The bacteria used to make yogurt are known as yogurt cultures. The fermentation of lactose by these bacteria produces lactic acid, which acts on milk protein to give yogurt its texture and characteristic tart flavor.'] ['yogurt food product'] +FOODON_03303909 ['A cultured dairy product is a fermented dairy product in which a microbial starter was introduced to the fermentation process.'] "[""SIREN DB annotation:\n* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913)\n* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119)\n ""]" ['cultured dairy product'] +FOODON_00001078 ['A food product having fermented soyabeans as a defining ingredient'] ['fermented soybean food product'] +FOODON_00001009 ['A hot dog is a moist sausage of soft, even texture and flavor, often made from advanced meat recovery or meat slurry. Most types are fully cooked, cured or smoked. It is often placed hot in a special purpose soft, sliced hot dog bun.'] ['hotdog'] ['hot dog'] ['frankfurter'] +FOODON_03420156 ['Soft sugar whose crystals are covered by a film of refined dark syrup that imparts color, flavor, and moisture.'] ['brown sugar'] +FOODON_03420108 "[""A broad term that includes the nutritive sweeteners dextrose, fructose, galactose, lactose, maltose and sucrose, which are simple carbohydrates with molecules composed of one or two saccharide units. Note that on a product label or in a recipe, 'sugar' means *SUCROSE* and should be so indexed. Use the broad term *SUGAR* only if the specific sugar used is not known or not listed in the vocabulary.""]" ['sugar'] +FOODON_03400115 ['Natural cheese, cured or uncured, cheese product (which is further processed), or cheese product analog.'] ['cheese or cheese product (us cfr)'] +FOODON_03400148 ['Milk in all forms, milk-based beverage, cultured milk product, or milk or milk product analog. Index infant formula under *MEAL REPLACEMENT*.'] ['milk or milk product (us cfr)'] +FOODON_03400143 ['Fruit in all forms; includes fruit juices and fruit juice drinks, fruit butters, jellies, preserves, and related products.'] ['fruit or fruit product (us cfr)'] +FOODON_03400204 ['Food product prepared by heating a mixture of sweeteners and other optional ingredients according to the specific formula for each subgroup.'] ['candy (us cfr)'] +FOODON_03400650 "['Vegetables are foods derived from many different kinds of plants mostly annual and usually cultivated, commonly known by custom and tradition as ""vegetables"".\nIn several countries, some of these commodities grown on large areas are distinguished as ""field crops"" or arable crops e.g. sugar beet. For the sake of convenience in this guide such crops are classified under Type 2 Vegetables.\nExposure to pesticides is dependent on the particular part of the plant used for food and the growing practices.\nVegetables may be consumed in whole or in part and in the form of fresh, dried or processed foods.']" ['02 vegetables (ccpr)'] +FOODON_03400803 ['includes fish offal; a food product whose predominant constituent is fish (e.g. dried and salted fish, smoked fish, canned fish, pickled fish, restructured fish and fish analogues, surimi; fish paste, pâté).'] ['seafood product (eurofir)'] +FOODON_03400842 ['Beverage containing no more than 0.5% alcohol; it may be flavoured, sweetened or carbonated; includes soft drinks and steeped beverages; excludes milk in all forms, fruit juices and vegetable juices.'] ['non alcoholic beverage (eurofir)'] +FOODON_03400861 ['This subgroup includes multicomponent meals, sauces, retail salads, desserts, soups, snacks and other foods where similarity of the product type is more significant than the source of the principal ingredient(s).'] ['prepared food product (eurofir)'] +FOODON_00001222 ['A sausage made from meats that have not been previously cured.'] ['sausage (raw)'] +FOODON_00001223 ['A cured sausage that is fermented and dried.'] ['sausage (dried, fermented)'] +FOODON_00001016 ['Cabbage or headed cabbage (comprising several cultivars of Brassica oleracea) is a leafy green or purple biennial plant, grown as an annual vegetable crop for its dense-leaved heads.'] ['cabbage food product'] +FOODON_00001151 ['A citrus fruit is botanically classified as a type of berry called a hesperidium that has a thick, leathery rind, with numerous oil glands, and a large flesh portion composed of several wedge-shaped sections. Unlike pome fruit, such as the apple, the citrus fruit is derived from a superior ovary, an ovary completely separate from the calyx.'] ['citrus fruit food product'] ['citrus'] +FOODON_00002141 ['A plant fruit food product which is labeled (in common language or by regulation) as a vegetable food product.'] ['plant fruit as vegetable food product'] +FOODON_00001635 ['A bean vegetable food product is a human or animal food product - such as a snap, shell or dry bean product - derived from the fruit pod, seed, or leaf of one of several genera of the flowering plant family Fabaceae.'] ['bean food product'] "['Note, this was previously labelled ""Bean (vegetable) food product"". We have been listing both dry and freshly harvested moist beans here, so have broadened the name scope.']" +FOODON_00001197 ['A bambara groundnut food product is a product derived from fresh or dried beans of the bambara groundnut plant.'] ['bambara groundnut food product'] ['Bambara nut', 'Bambara-bean', 'Congo goober', 'earth pea', 'ground-bean', 'hog-peanut'] +FOODON_00001200 ['A product of the dry seeds of Vigna unguiculata.'] ['cowpea (pulse) food product'] +FOODON_00001003 ['The juice products which are made from the fermented sap of the maguey (agave) plant.'] ['fermented agave juice'] +FOODON_00001148 ['A potato food product is any product derived from potatoes.'] ['potato food product'] +FOODON_00001164 ['A food product deriving from one or more tomatoes.'] ['tomato food product'] +FOODON_00001209 "['PULSES are annual leguminous crops yielding from one to 12 grains or seeds of variable size, shape and colour within a pod. They are used for both food and feed. The term ""pulses"" is limited to crops harvested solely for dry grain, thereby excludingcrops harvested green for food (green peas, green beans, etc.) which are classified as vegetable crops. Also excluded are those crops used mainly for oil extraction (e.g.soybeand and groundnuts) and leguminous crops (e.g. seeds of clover and alfalfa) that are used exclusively for sowing purposes.']" ['pulse', 'pulses'] ['pulse food product'] +FOODON_00001994 ['A food product made from legumes that are considered vegetables, such as immature raw legume pods or seeds.'] ['leguminous vegetable food product'] +FOODON_00002780 ['A pigeon pea food product is a food product derived from the pigeon pea plant'] ['pigeon pea food product'] +FOODON_00001215 ['A food product derived from Theobroma cacao.'] ['cocoa and cocoa products'] ['cacao food product'] +FOODON_00001087 ['A lipid material derived from plants. Physically, oils are liquid at room temperature.'] ['vegetable oil food product'] +FOODON_00001138 ['A beverage product derived from leaves of the tea plant (Camellia sinensis).'] "['""While fermentation is also referred to in the production of brewed teas, this is inaccurate. Some herbal teas on the market today include probiotic cultures alongside tea leaves to maintain gut health but the tea itself hasn\'t been fermented. Most dried teas however don\'t use live cultures at all during production. Instead, harvested tea leaves undergo a natural chemical process known as oxidation, which also changes the color, flavor and level of health benefits in the resulting brew."" [https://eatcultured.com/blogs/our-awesome-blog/fermented-tea]']" ['tea based beverage product'] +FOODON_00001132 ['Suidae is a family of artiodactyl mammals which are commonly called pigs, hogs or boars. In addition to numerous fossil species, 17 extant species are currently recognized (or 18 counting domestic pigs and wild boars separately), classified into between four and eight genera. The family includes the domestic pig, Sus scrofa domesticus or Sus domesticus, in addition to numerous species of wild pig, such as babirusas and warthogs. All suids, or swine, are native to the Old World, ranging from Asia to Europe and Africa.'] ['swine food product'] +FOODON_03317170 ['A meat product is a product organized by the form of - or processing done to - its meat component (a skeletal meat part of an animal or crustacean).'] "[""SIREN DB annotation:\n* derives from 'animal body or body part' (http://purl.obolibrary.org/obo/FOODON_03420127)\n ""]" ['meat (whole or parts)'] +FOODON_00001013 ['Cheese is a food derived from milk that is produced in a wide range of flavors, textures, and forms by coagulation of the milk protein casein.'] ['cheese'] ['cheese food product'] +FOODON_00001105 ['A food product made from an avian egg.'] ['avian egg food product'] +FOODON_00001283 ['A food product from a category of domestic birds kept for meat, eggs, and feathers including fowl such as chickens, turkeys, and waterfowls such as domestic ducks and geese and other meat birds such as pigeons and doves and games birds including pheasants.'] ['poultry food product'] +FOODON_03315173 ['A fish product is a home-made or commercially produced or retail or wholesale product containing substantial amounts of freshwater or saltwater fish and/or shellfish flesh. Note that this category should avoid items that mention a particular species of fish or shellfish.'] "[""SIREN DB annotation:\n* derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175)\n ""]" ['fish product (unspecified species)'] +FOODON_00001104 ['This food product type includes food products which are made from eggs laid by the sea water fish.'] ['sea water fish egg food product'] +FOODON_00001050 ['A food product having tempeh as a defining ingredient'] ['tempeh food product'] +FOODON_00001070 ['A food produced by fermenting rice, barley and/or soybeans, with salt and the mold koji-kin (Aspergillus oryzae).'] "[""SIREN DB annotation:\n* has quality 'semisolid' (http://purl.obolibrary.org/obo/FOODON_03430144)\n* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014)\n* derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133)\n* formed as a result of 'fermentation/modification process, multiple component' (http://purl.obolibrary.org/obo/FOODON_03460128)\n* formed as a result of 'salted' (http://purl.obolibrary.org/obo/FOODON_03460173)\n* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253)\n* formed as a result of 'preservation by fermentation' (http://purl.obolibrary.org/obo/FOODON_03470104)""]" ['miso food product'] +FOODON_00002752 ['A whole dried bean is a bean resulting from natural or mechanical air drying applied to a bean or bean pod.'] ['dried bean'] ['bean (whole, dried)'] +FOODON_00001203 ['A product of the dry seeds of Vicia sativa.'] ['vetch seed (whole, dried)'] +FOODON_00001059 ['Apple juice is a fruit juice made by the maceration and pressing of an apple.'] ['apple juice'] ['apple juice'] +FOODON_03400187 ['Cheese made from milk or milk components, such as cream, by the following process: (1) produce curd through coagulation of milk by bacterial action and/or enzymes and/or acidification and draining of whey. (2) For cured cheese only: cure the curd. Excludes products made through further processing, such as comminuting (see *CHEESE PRODUCT*).'] ['natural cheese (us cfr)'] +FOODON_03400147 ['Food product having functional characteristics similar to milk or milk products, including cream product analogs, margarine, and milk analogs. Certain alternate ingredients are substituted for those components that are responsible for specific functional properties.'] ['milk or milk product analog (us cfr)'] +FOODON_03400155 ['Semisolid or jelled food prepared from fruit or fruit juice and other ingredients prescribed for the individual products (21 CFR 150).'] ['fruit butter, jelly, preserve or related product (us cfr)'] +FOODON_03400293 ['Candy prepared by cooking a mixture of water, sugars and optional ingredients to a temperature of 250 degrees F. or less.'] ['soft candy (us cfr)'] +FOODON_03400680 ['Pulses are derived from the mature seeds naturally or artificially dried, of leguminous plants known as beans (dry) and peas (dry).\nThe seeds in the pods are protected from most pesticides applied during the growing season except pesticides which show a systemic action. The dried beans and peas however are often exposed to post-harvest treatments.\nThe dry pulses are consumed after processing or household cooking.'] ['015 pulses (vd) (ccpr)'] +FOODON_03400845 ['Beverage prepared by extracting flavour and other components from food sources by percolation and/or immersion in water, usually at near-boiling temperature. The group includes coffee (e.g. instant coffee, coffee and chicory essence), tea, herbal tea (e.g. green tea, black tea, tisane), cocoa beverage and beverage powder.'] ['LanguaL curation note: Renamed from *COFFEE, TEA, COCOA (EUROFIR)* (LanguaL 2010).'] ['coffee, tea, cocoa or infusion (eurofir)'] +FOODON_03400865 ['A liquid food made by simmering meat, poultry, seafood or vegetables, being clear or thickened to the consistency of a thin puree or having milk or cream added, and often containing pieces of solid food such as meat, shellfish, pasta or vegetables. Soup takes precedence over other food products. Examples are egg and lemon soup, oxtail soup, fish soup, rice soup, lentil soup, minestrone, cherry soup.'] ['soup (eurofir)'] +FOODON_00002266 ['A soybean food product is a product derived from the soybean plant.'] ['soy product'] ['soybean food product'] +FOODON_00001194 ['A product of the dry seeds of plants of the genus Pisum.'] ['dry pea food product'] +FOODON_03301467 ['A bean substance is a substance made by processing seed from a bean plant.'] "[""SIREN DB annotation:\n* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155)\n ""]" ['bean substance'] "[""Damion Dooley's note: This class is intended to provide the most generic reference to bean, as it does not imply any more information about the state of a bean - whether it is whole or in fragments, or fragments of several beans, whether it is dry, raw, or cooked etc.""]" +FOODON_00001202 ['The winged bean food category covers beans of the winged bean plant'] ['winged bean food product'] +FOODON_00001204 "['Pachyrhizus erosus, commonly known as jicama Mexican yam bean, or Mexican turnip, is the name of a native Mexican vine, although the name most commonly refers to the plant\'s edible tuberous root. Jícama is a species in the genus Pachyrhizus in the bean family (Fabaceae). Plants in this genus are commonly referred to as yam bean, although the term ""yam bean"" can be another name for jícama.\n\nIn contrast to the root, the remainder of the jícama plant is very poisonous; the seeds contain the toxin rotenone, which is used to poison insects and fish.\n\nFAO: The yam bean is a legume but unlike its close relatives the soybean and other beans, the yam bean is cultivated for its large, tuberous roots.']" ['yam bean food product'] +FOODON_00001665 ['A broad bean food product is a product derived from the broad bean plant.'] ['broad bean food product'] +FOODON_00002753 ['A seed of a bean plant from one of several genera of the flowering plant family (Fabaceae).'] ['bean'] ['bean (whole)'] "[""Damion Dooley's note. This could be enhanced to explicitly state the anatomical parts of a seed - seed coat, cotyledons, embryo etc. Currently the Plant Ontology is not explicit about this yet.""]" +FOODON_00004156 ['A bean food product made from velvet bean.'] ['velvet bean food product'] +FOODON_00002791 ['A seed of a vetch plant.'] ['vetch seed'] ['vetch seed (whole)'] +FOODON_00001198 ['A product of the dry seeds of plants of the genus Vicia.'] ['dried fava bean'] ['broad bean (whole, dried)'] ['http://en.wikipedia.org/wiki/Legume'] +FOODON_00001199 ['A product of the dry seeds of Cicer arietinum.'] ['garbanzo bean food product'] ['chickpea food product'] ['Bengal gram', 'Egyptian pea', 'gram'] +FOODON_00001201 ['A dry bean food product refers to a bean product made from a Phaseolus species plant whose seeds are harvested at complete maturity.'] "['FAO notes: ""Only species of Phaseolus should be included, though several countries also include certain types of beans. Commonly classified as Vigna (angularis, mungo, radiata, aconitifolia). In the past, these species were also classified as Phaseolus.""']" ['dry bean food product'] ['kidney, haricot bean (Ph. vulgaris); \nlima, butter bean (Ph. lunatus); \nadzuki bean (Ph. angularis); \nmungo bean, golden, green gram (Ph. aureus); \nblack gram, urd (Ph. mungo); \nscarlet runner bean (Ph. coccineus); \nrice bean (Ph. calcaratus); \nmoth bean (Ph. aconitifolius); \ntepary bean (Ph. acutifolius)'] +FOODON_00001205 ['A product of the dry seeds of Mucuna pruriens var. utilis.'] ['velvet bean (whole, dried)'] +FOODON_00001207 ['A dry seed of the jack-bean plant.'] ['jack bean (whole, dried)'] +FOODON_00002115 ['A product containing primarily immature ripe pigeon peas.'] ['pigeon pea vegetable food product'] +FOODON_00001056 ['A fine powder made from cereals or other starchy food sources.'] ['flour food product'] +FOODON_00001088 ['An oil used as a nutritional supplement and is a traditional European ethnic food, highly regarded for its nutty flavor.'] ['flax oil', 'flax seed oil', 'linseed oil', 'linseed oil'] ['Food-grade flaxseed oil is cold-pressed, obtained without solvent extraction, in the absence of oxygen, and marketed as edible flaxseed oil.[wikipedia]'] ['flaxseed oil'] +FOODON_03420307 ['The oil produced by pressing or extracting lipids from plant seeds (e.g. grapeseed oil, rapeseed oil, linseed oil) /AM'] ['seed oil'] +FOODON_00001004 ['This food product type includes food products which are made from fermentation of juice extracted from pressed sugarcane.'] ['fermenting sugar cane juice'] +FOODON_00001260 ['Beer is a fermented cereal beverage resulting from the fermentation most commonly of malted barley (though wheat, corn, or rice may included), by a yeast, most commonly Saccharomyces cerevisiae, and flavored by dried flowers of hops, Humulus lupulus.'] ['beer beverage'] +FOODON_00001245 ['A beverage prepared from the cured leaves of Camellia sinensis by combination with hot or boiling water.'] ['tea beverage (liquid)'] +FOODON_00001244 ['A brewed drink prepared from roasted seeds, commonly called coffee beans, of the coffee plant.'] ['coffee beverage'] +FOODON_00001275 ['A hen egg food product is any food product consisting mainly of hen eggs or derivatives.'] ['hen egg food product'] +FOODON_00001131 ['A food product made from domesticated bird meat.'] ['poultry meat food product'] +FOODON_00001276 ['Cider, hard apple cider, or hard cider in the US, is an alcoholic beverage made from the fermented juice of apples.'] ['cider'] ['apple cider (alcoholic)'] +FOODON_00001196 ['A product of the dry seeds of Cajanus cajan.'] ['pigeon pea (whole, dried)'] +FOODON_03400294 ['Food product having functional characteristics similar to a butter product; it may be nutritionally equivalent or inferior to the product it purports to resemble.'] ['butter product analog (us cfr)'] +FOODON_03400209 ['Jelled product made from one or more fruit juices and optional ingredients. Includes both fruit jelly, which may be sweetened with nutritive carbohydrate sweeteners, (21 CFR 150.140), and artificially sweetened fruit jelly (21 CFR 150.141). The finished fruit jelly must have a soluble solid content of no less than 65% and the ratio by weight of the fruit ingredient to sweetener in the starting mixture must be no less than 45:55. Artificially sweetened fruit jelly must contain no less than 55% fruit ingredient by weight.'] ['fruit jelly (us cfr)'] +FOODON_03400213 ['Soft candy prepared by boiling milk, sugar, salt and optional ingredients to the soft-ball stage (238 degrees F.).'] ['fudge (us cfr)'] +FOODON_00001071 ['A grape berry food product which is the juice of freshly pressed grapes that contains some amount of pulp, skins, stems, and seeds.'] ['Grape pomace components typically comprises between 7 to 23 percent of the total weight of must. [https://en.wikipedia.org/wiki/Must]'] ['grape must'] +FOODON_00001152 ['The fleshy fruit (false berry) of a plant of the family Cucurbitaceae.'] ['melon fruit food product'] +FOODON_03301227 ['A seed of a broad bean plant (Vicia faba).'] ['Windsor bean', 'broad bean', 'broadbean', 'faba bean', 'fava bean'] ['broad bean (whole)'] ['Horse bean', 'field bean', 'tic bean', 'tick bean'] +FOODON_00002786 ['A seed of a velvet bean plant (Mucuna pruriens)'] ['tericopelo bean', 'tericopelo bean', 'velvet bean'] ['velvet bean (whole)'] +FOODON_00002778 ['A seed of a jack seed plant (Canavalia ensiformis).'] ['jack bean'] ['jack bean (whole)'] +FOODON_00002781 ['A seed of a pigeon pea plant (Cajanus cajan).'] ['pigeon pea'] ['pigeon pea (whole)'] +FOODON_00001076 ['Sake is a fermented rice beverage resulting from the fermentation of rice with the mold Aspergillus oryzae and, in parallel, with the yeast Saccharomyces cerevisiae [wikipedia:sake]'] ['sake food product'] +FOODON_00001282 ['A ground beef product is made of beef that has been finely chopped with a knife or a meat grinder (American English) or mincing machine (British English). Ground beef is used in many recipes including hamburgers and spaghetti Bolognese.'] ['beef mince', 'hamburger meat', 'minced beef', 'beef mince', 'ground beef'] ['ground beef food product'] +FOODON_00001038 ['A food product made from domestic pig meat (Sus domesticus or Sus scrofa scrofa).'] ['pork'] ['pork meat food product'] +FOODON_00002819 ['A liver food product is a food product that derives from one or more liver organs.'] ['liver food product'] +FOODON_03420244 ['The serum or watery part of milk that is separated from the thicker or more coagulable part or curd, espcially in the process of making cheese; it contains lactose, minerals and lactalbumin.'] ['whey'] ['mammalian milk whey'] +FOODON_00001286 ['A turkey meat food product is any food product made predominantly of turkey parts.'] ['turkey meat food product'] +FOODON_03400231 ['Food product having functional characteristics similar to those of butter; it is in plastic form or liquid emulsion and contains not less than 80% fat whose origin is vegetable or rendered animal carcass fats or a mixture of these as well as other optional ingredients specified by 21 CFR 166.110.'] ['margarine (us cfr)'] +FOODON_00001154 ['Citrullus lanatus is a plant species in the family Cucurbitaceae, a vine-like (scrambler and trailer) flowering plant originally from sub-Saharan Africa. It is cultivated for its fruit. The subdivision of this species into two varieties, watermelons (Citrullus lanatus (Thunb.) var. lanatus) and citron melons (Citrullus lanatus var. citroides (L. H. Bailey) Mansf.)'] ['citrullus lanatus fruit food product'] +FOODON_00001295 ['A family of hard Italian cheeses made from sheep milk.'] ['pecorino cheese'] +FOODON_00001288 ['Cantaloupe (also known as muskmelon (India and the United States), mushmelon, rockmelon (in Australian states and in New Zealand), sweet melon, spanspek (South Africa), or capuchin (Scotland) refers to a variety of the Cucumis melo species in the Cucurbitaceae family.'] ['cantaloup', 'muskmelon'] ['cantaloupe fruit food product'] +FOODON_00001128 "[""A very strong smelling, soft cow's milk cheese made by fermentation involving the bacterium Brevibacterium linens.""]" ['Limburger cheese food product'] +ENVO_01000478 ['cement render', 'cement stucco'] ['cement plaster'] +ENVO_00002186 ['polluted water'] ['contaminated water'] +FOODON_00001181 ['cooked'] ['food (cooked)'] +FOODON_03303220 ['desert preparation', 'dessert'] "[""SIREN DB annotation:\n* has substance added 'sugar or sugar syrup added' (http://purl.obolibrary.org/obo/FOODON_03460136)\n ""]" ['dessert food'] +FOODON_00001094 ['alcoholic beverage'] "[""SIREN DB annotation:\n* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130)\n* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119)\n* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253)\n ""]" ['fermented beverage'] +FOODON_00002456 ['baked', 'baked food product'] ['food (baked)'] +FOODON_00001045 ['ice-cream', 'ice cream'] ['ice cream food product'] +FOODON_03315552 ['juice'] ['juice beverage'] +FOODON_00001146 ['tuber'] ['solanaceous root food product'] +FOODON_00001158 ['pomes'] ['pomaceous fruit food product'] +FOODON_00001859 ['linseed food product'] ['flaxseed food product'] +FOODON_00001139 ['coffee and coffee products'] ['coffee based beverage product'] +FOODON_00002044 ['mollusk food product'] ['mollusc food product'] +FOODON_00001098 ['fermented apple'] ['fermented apple beverage'] +FOODON_00002012 ['lupin'] ['lupine bean food product'] +FOODON_00001189 ['common oat food product'] ['oat food product'] +ENVO_0010003 ['This is quite odd and it probably should be obsoleted. Any material that is a participant in an agricultural process can be seen as an agricultural material.'] ['agricultural environmental material'] ['This class will be depopulated and eventually deprecated. Convenience class.'] +ENVO_01001189 ['An organic material which is primarily composed of living or dead algae, along with their exudates.'] ['algal material'] "['This class will be axiomatised with ""alga"" once an approach to handle this term\'s ambiguous semantics has been agreed with PCO.']" +FOODON_03460177 ['LanguaL curation note: With the exception of peanut (see *PEANUT OR PEANUT BUTTER ADDED*), used when a nut or seed ingredient is the second ingredient in order of predominance.'] ['plant seed or nut food product'] ['This disjunction is provided for food indexers who used the LanguaL category per guidelines. Currently, by specifying the more specific nut or seed as ingredient instead, this category can be inferred.'] +ENVO_01001391 ['An organic environmental material which is primarily composed of gill tissue.'] ['gill tissue material'] +ENVO_01000838 ['Smoke is a collection of airborne solid and liquid particulates and gases emitted when a material undergoes combustion or pyrolysis, together with the quantity of gas that is entrained or otherwise mixed into the mass'] ['smoke'] +ENVO_01001511 ['Water ice which is formed by the freezing of fresh water.'] ['freshwater ice'] +ENVO_00005788 ['Soil which is part of a rubber plantation.'] ['rubber plantation soil'] +ENVO_01001392 ['Gill tissue material which is part of salt-water mussel in the family Mytilidae'] ['mussel gill tissue material'] +ENVO_00002127 ['Revise adjacent to. Consider sampled stream sediment. Dry stream sediment.'] ['stream sediment'] +FOODON_03400356 ['LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term.'] ['European Union agency food product type'] +ENVO_02000106 ['Dust which is derived from asbestos'] ['asbestos dust'] +ENVO_01001393 ['Mussel gill tissue material which is part of a member of the genus Bathymodiolus.'] ['Bathymodiolus gill tissue material'] +FOODON_03316579 "[""SIREN DB annotation:\n* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174)\n ""]" ['multi-component plant food product'] +FOODON_03400777 ['LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term.'] ['eurofir food classification'] +FOODON_03315925 "[""SIREN DB annotation:\n* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151)\n* derives from 'meat part of animal' (http://purl.obolibrary.org/obo/FOODON_03420103)\n ""]" ['pate'] +FOODON_03302001 "[""SIREN DB annotation:\n* derives from 'part of animal' (http://purl.obolibrary.org/obo/FOODON_03420164)\n ""]" ['animal-derived food'] +FOODON_03310006 "[""SIREN DB annotation:\n* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155)\n* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119)\n* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253)\n ""]" ['fermented bean product'] +FOODON_03305536 "[""SIREN DB annotation:\n* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139)\n* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014)\n* derives from 'sugar syrup or syrup solids' (http://purl.obolibrary.org/obo/FOODON_03420271)\n* has substance added 'honey added' (http://purl.obolibrary.org/obo/FOODON_03460149)\n ""]" ['honey blend table syrup'] +FOODON_03400644 ['LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term.'] ['a. primary food commodities of plant origin (ccpr)'] +FOODON_00001008 "[""SIREN DB annotation:\n* has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119)\n* derives from 'liver' (http://purl.obolibrary.org/obo/UBERON_0002107)\n ""]" ['liver paste'] +FOODON_03301444 "[""SIREN DB annotation:\n* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130)\n* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174)\n ""]" ['vegetable juice food product'] +FOODON_00001274 ['Regarding American regulatory aspects of egg products, see this summary:\nhttps://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-graphic-000077'] ['egg food product'] +FOODON_03307539 "[""SIREN DB annotation:\n* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138)\n* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116)\n ""]" ['food (dried)'] +FOODON_03302082 "[""SIREN DB annotation:\n* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151)\n* derives from 'skeletal meat part, without bone or shell' (http://purl.obolibrary.org/obo/FOODON_03420125)\n* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138)\n* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116)\n ""]" ['beef (dehydrated)'] +FOODON_03312053 "[""SIREN DB annotation:\n* has quality 'divided or disintegrated' (http://purl.obolibrary.org/obo/FOODON_03430122)\n* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014)\n* derives from 'skeletal meat part, without bone, without skin' (http://purl.obolibrary.org/obo/FOODON_03420268)\n* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119)\n* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138)\n* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116)\n ""]" ['pork (dehydrated)'] +FOODON_03310387 "[""SIREN DB annotation:\n* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139)\n* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190)\n ""]" ['oil'] +FOODON_03316694 "[""SIREN DB annotation:\n* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190)\n ""]" ['vegetable fat food product'] +FOODON_03304497 "[""SIREN DB annotation:\n* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150)\n* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155)\n ""]" ['edible seed food product'] +FOODON_03316079 "[""SIREN DB annotation:\n* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130)\n* has quality 'heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440022)\n* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174)\n* formed as a result of 'steeping' (http://purl.obolibrary.org/obo/FOODON_03450036)\n ""]" ['herbal infusion'] +FOODON_03316271 "[""SIREN DB annotation:\n* derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108)\n ""]" ['sugar product'] +FOODON_03460231 ['LanguaL curation note: Used when chocolate or cocoa is added at any level or when chocolate is used as a coating.'] ['chocolate or cocoa'] +FOODON_00001065 "[""SIREN DB annotation:\n* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151)\n* derives from 'curd' (http://purl.obolibrary.org/obo/FOODON_03420245)\n* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253)\n* formed as a result of 'interior mold curing process' (http://purl.obolibrary.org/obo/FOODON_03460331)""]" ['blue cheese food product'] +FOODON_03315150 "[""SIREN DB annotation:\n* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913)\n ""]" ['mammalian milk product'] +FOODON_03307345 "[""SIREN DB annotation:\n* has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143)\n* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014)\n* derives from 'white sugar' (http://purl.obolibrary.org/obo/FOODON_03420157)\n ""]" ['sugar (refined)'] +FOODON_00001100 "[""SIREN DB annotation:\n* has quality 'liquid, low viscosity' (http://purl.obolibrary.org/obo/FOODON_03430109)\n* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200)\n* has substance added 'water addition process' (http://purl.obolibrary.org/obo/FOODON_03460148)\n* has substance added 'sweetener added' (http://purl.obolibrary.org/obo/FOODON_03460202)\n* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227)\n ""]" ['orange fruit beverage'] +FOODON_03315302 "[""SIREN DB annotation:\n* derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133)\n* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119)\n* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253)\n ""]" ['cocoa food product'] +FOODON_03301073 "[""SIREN DB annotation:\n* has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143)\n* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014)\n* derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108)\n* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138)\n* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116)\n ""]" ['sugar (granulated)'] +FOODON_03301103 "[""SIREN DB annotation:\n* has quality 'liquid, low viscosity, with small particles' (http://purl.obolibrary.org/obo/FOODON_03430114)\n* derives from 'fruit, peel removed, core, pit or seed removed' (http://purl.obolibrary.org/obo/FOODON_03420229)\n ""]" ['orange juice'] +ENVO_00002873 ['organic waste material'] ['This should probably be merged with biological waste material.'] ['organic waste'] +ENVO_00002276 ['animal waste material'] "[""This will become a defined class, with subclasses added through inference based on material having a 'waste role' and being associated with animal metabolism.""]" ['animal waste'] +FOODON_00001258 ['food (fermented)'] ['Are all fermented foods considered preserved to some extent?'] +FOODON_00001172 ['nut food product'] "['The default nut product is a whole, raw nut - meaning that the kernel is whole, and moderately or significantly dried, but not baked. Minimal references to nuts often leave ambiguous whether the shell is on or off. ""I ate a peanut"" doesn\'t clarify whether I ate a shell-off nut or whether I did the shelling.']" +ENVO_00002206 ['coal mine waste material'] ['coal mine waste'] ['coal refuse'] +ENVO_00002266 ['chicken breeding waste material'] ['chicken breeding waste'] ['chicken yard waste'] +ENVO_00002207 ['self-heating coal mine waste material'] ['self-heating coal mine waste'] +FOODON_00002158 ['food (preserved)'] ['preserved'] +ENVO_00003903 ['aviation fuel'] ['jet fuel'] +FOODON_00001063 ['millet beer food product'] ['bantu beer'] +ENVO_2000045 ['hydrocarbon-based environmental material'] +ENVO_01001644 ['material primarily composed of biogenic carbonates'] +ENVO_00002040 ['wood'] +ENVO_01001820 ['cultured organic material'] +ENVO_00002192 ['poultry litter'] +ENVO_01000558 ['liquefied hydrocarbon gas'] +ENVO_00005794 ['water scum'] +ENVO_00002046 ['activated sludge'] +ENVO_00002057 ['raw primary sludge'] +ENVO_00002058 ['secondary sludge'] +ENVO_00002176 ['contaminated sludge'] +ENVO_00002129 ['anaerobic sludge'] +ENVO_00002212 ['thermophilic granular sludge'] +ENVO_00005796 ['marine sludge'] +ENVO_01000508 ['salt material'] +ENVO_02000104 ['cement dust'] +ENVO_02000109 ['dust from plant parts'] +ENVO_00002135 ['treated wood'] +ENVO_00002193 ['pulp-bleaching waste water'] +ENVO_00002138 ['beach sand'] +ENVO_00005798 ['acid dune sand'] +ENVO_00002118 ['sea sand'] +ENVO_00005799 ['rocky sand'] +ENVO_00002179 ['intertidal sediment'] +ENVO_00002171 ['hay compost'] +ENVO_00003032 ['fresh animal manure'] +ENVO_00003859 ['horse manure'] +ENVO_00003884 ['farmyard manure'] +ENVO_00003927 ['stable manure'] +ENVO_02000084 ['goat manure'] +ENVO_00003908 ['poultry deep litter'] +FOODON_03311737 ['processed food product'] +ENVO_00002177 ['1,4-dioxane contaminated sludge'] +ENVO_00003965 ['anaerobic digester sludge'] +ENVO_00003071 ['grass silage'] +ENVO_00003978 ['potato silage'] +ENVO_00003870 ['rice straw'] +ENVO_02000098 ['platinum ore'] +ENVO_02000097 ['gold ore'] +ENVO_02000096 ['iron ore'] +ENVO_02000111 ['copper ore'] +ENVO_02000102 ['fibrous glass dust'] +ENVO_02000108 ['cotton dust'] +ENVO_00002136 ['arsenate treated wood'] +ENVO_01001847 ['hoarfrost'] +ENVO_01001849 ['glaze'] +ENVO_00002148 ['coarse beach sand'] +ENVO_00002134 ['anaerobic stream sediment'] +ENVO_00002154 ['radioactive sediment'] +ENVO_02000113 ['welding fume'] +ENVO_02000114 ['paraffin wax fume'] +ENVO_02000120 ['zinc chloride fume'] +ENVO_00002159 ['drilling bore water'] +ENVO_00002194 ['oil field production water'] +ENVO_00003065 ['distilled water'] +ENVO_00003097 ['bore hole water'] +ENVO_00005793 ['muddy water'] +FOODON_00001010 ['processed meat food product'] +FOODON_00001229 ['processed cheese food product'] +FOODON_00002196 ['refined or partially-refined food product'] +FOODON_00001626 ['bakery food product'] +FOODON_00001857 ['food flavoring or seasoning product'] +FOODON_00001867 ['food dressing product'] +FOODON_00002219 ['salad food product'] +FOODON_00002450 ['multi-component honey product'] +ENVO_00003900 ['rye grass silage'] +ENVO_2000009 ['sub-bitumous coal'] +ENVO_00002155 ['high-level radioactive sediment'] +ENVO_02000116 ['aluminum welding fume'] +ENVO_00002158 ['ditch water'] +ENVO_00002228 ['pond water'] +ENVO_00003096 ['tap water'] +ENVO_00002142 ['borax leachate'] +ENVO_01000599 ['river water'] +FOODON_00001039 ['cured meat food product'] +FOODON_00001241 ['processed pork meat food product'] +FOODON_00002131 ['plant based refined or partially-refined food product'] +FOODON_00002423 ['agave food product'] +FOODON_00001165 ['solanaceous food product'] +FOODON_00001166 ['plant inflorescence food product'] +FOODON_00001169 ['cruciferous food product'] +FOODON_00001262 ['botanical fruit food product'] +FOODON_00001174 ['plant lipid food product'] +FOODON_00001175 ['plant stem food product'] +FOODON_00001253 ['plant derived beverage'] +FOODON_00001243 ['animal lipid food product'] +FOODON_00001176 ['invertebrate animal food product'] +FOODON_00001252 ['animal derived beverage'] +FOODON_00001053 ['fermented dairy food product'] +FOODON_00001054 ['fermented fish or seafood food product'] +FOODON_00001069 ['fermented fruit food product'] +FOODON_00001073 ['vinegar food product'] +FOODON_00002333 ['vegetable pickle food product'] +FOODON_00002125 ['plant based bakery food product'] +FOODON_00001278 ['cake food product'] +FOODON_00001083 ['sugar condiment'] +FOODON_00002300 ['sweetener food product'] +FOODON_00002262 ['soybean condiment'] +FOODON_00001610 ['apple condiment'] +FOODON_00002146 ['plant product dressing'] +FOODON_00001280 ['chocolate food product'] +FOODON_00001279 ['cake icing food product'] +FOODON_00001800 ['dairy dessert food product'] +FOODON_00002132 ['plant based salad food product'] +FOODON_00003395 ['multi-component wheat food product'] +FOODON_00002126 ['plant-based candy'] +FOODON_03400960 ['50220000 - cereal/grain/pulse products (gs1 gpc)'] +FOODON_03401061 ['50190000 - prepared/preserved foods (gs1 gpc)'] +FOODON_00002301 ['pork cured meat food product'] +FOODON_00001225 ['smoked meat food product'] +FOODON_00001696 ['cattle cured meat food product'] +FOODON_00002153 ['plant seed vegetable food product'] +FOODON_00001783 ['cowpea vegetable food product'] +FOODON_00002156 ['plant stem or spear vegetable food product'] +FOODON_00001089 ['corn flour food product'] +FOODON_00001163 ['solanaceous fruit food product'] +FOODON_00001171 ['cruciferous inflorescence food product'] +FOODON_00001182 ['pickled cruciferous food product'] +FOODON_00001173 ['plant seed food product'] +FOODON_00001254 ['plant derived fermented beverage'] +FOODON_00001255 ['nonfermented plant derived beverage product'] +FOODON_00002275 ['steeped beverage product'] +FOODON_00001747 ['cocoa beverage'] +FOODON_00001251 ['avian food product'] +FOODON_00001055 ['sea water fish food product'] +FOODON_00001293 ['shellfish food product'] +FOODON_00001177 ['insect food product'] +FOODON_00001217 ['mammalian milk beverage'] +FOODON_00001159 ['fermented pomaceous fruit beverage'] +FOODON_00001919 ['grain based vinegar food product'] +FOODON_00001613 ['apple vinegar food product'] +FOODON_00002364 ['wine or wine-like food product'] +FOODON_00001219 ['sausage (cooked, smoked)'] +FOODON_00001183 ['bread food product'] +FOODON_00001212 ['pastry food product'] +FOODON_00002151 ['plant seed based bakery food product'] +FOODON_00001178 ['honey food product'] +FOODON_00002157 ['plant sweetener'] +FOODON_00001231 ['creamy salad dressing'] +FOODON_00001232 ['vinaigrette dressing food product'] +FOODON_00001235 ['soy sauce food product'] +FOODON_00001140 ['fruit juice food product'] +FOODON_00001878 ['frozen dairy dessert'] +FOODON_00002035 ['milk dessert food product'] +FOODON_00001289 ['potato salad food product'] +FOODON_00001891 ['fruit salad food product'] +FOODON_00001001 ['orange juice (liquid)'] +FOODON_03400969 ['50221200 - processed cereal products (gs1 gpc)'] +FOODON_03401095 ['50192900 - pasta/noodles (gs1 gpc)'] +ENVO_00003045 ['bacon curing brine'] +FOODON_00001220 ['sausage (smoked)'] +FOODON_00001077 ['salt pork meat food product'] +FOODON_00002053 ['mustard food product'] +FOODON_00001058 ['fruit extract food product'] +FOODON_00001150 ['cucurbit fruit food product'] +FOODON_00001640 ['berry food product'] +FOODON_00002787 ['vetch food product'] +FOODON_00001024 ['pickled cabbage food product'] +FOODON_00002813 ['pea food product'] +FOODON_00001093 ['cereal grain food product'] +FOODON_00001097 ['fermented sugar cane beverage'] +FOODON_00001096 ['fermented elaeis palm beverage'] +FOODON_00001102 ['fermented grain beverage'] +FOODON_00001838 ['fermented cereal beverage'] +FOODON_00001136 ['distilled fermented beverage'] +FOODON_00001246 ['hot chocolate food product'] +FOODON_00001247 ['mate food product'] +FOODON_00001675 ['cabbage juice food product'] +FOODON_00002316 ['tomato juice food product'] +FOODON_00001134 ['bovine meat food product'] +FOODON_00001257 ['milk or milk based food product'] +FOODON_00001107 ['bovine dairy food product'] +FOODON_00001106 ['camelid dairy food product'] +FOODON_00001111 ['equine dairy food product'] +FOODON_00001879 ['frozen dairy food product'] +FOODON_00001250 ['fish egg food product'] +FOODON_00001218 ['bee food product'] +FOODON_00001090 ['sour milk beverage'] +FOODON_00001120 ['camelid milk beverage'] +FOODON_00001121 ['equine milk beverage'] +FOODON_00001017 ['commercial yogurt'] +FOODON_00001086 ['kefir food product'] +FOODON_00001074 ['barley malt vinegar'] +FOODON_00001259 ['non-fruit wine food product'] +FOODON_00001091 ['dried milk food product'] +FOODON_00001234 ['mayonnaise food product'] +FOODON_00001157 ['pomaceous fruit juice beverage'] +FOODON_00001156 ['citrus fruit juice'] +FOODON_00001777 ['cow milk dessert'] +FOODON_00001277 ['orange juice (unpasteurized)'] +FOODON_00001221 ['sausage (raw, smoked)'] +FOODON_00001162 ['grape extract'] +FOODON_00001160 ['pomaceous fruit extract'] +FOODON_00001161 ['citrus fruit extract food product'] +FOODON_00002029 ['melon food product'] +FOODON_00002071 ['orange food product'] +FOODON_00001611 ['apple food product'] +FOODON_00001170 ['grape berry food product'] +FOODON_00001757 ['common bean food product'] +FOODON_00001208 ['hyacinth bean food product'] +FOODON_00002779 ['jack-bean food product'] +FOODON_00001206 ['lupin seed food product'] +FOODON_00001191 ['barley food product'] +FOODON_00001141 ['wheat food product'] +FOODON_00001185 ['rice food product'] +FOODON_00001186 ['buckewheat food product'] +FOODON_00001187 ['sorghum food product'] +FOODON_00001190 ['rye food product'] +FOODON_00001192 ['quinoa food product'] +FOODON_00002038 ['millet food product'] +FOODON_00002265 ['soybean seed (field) food product'] +FOODON_00001233 ['nut oil food product'] +FOODON_00001005 ['fermenting elaeis palm sap food product'] +FOODON_00001019 ['wort food product'] +FOODON_00001051 ['fermented rice beverage'] +FOODON_00001062 ['fermented millet food product'] +FOODON_00001135 ['distilled fermented grain beverage'] +FOODON_00001041 ['beef food product'] +FOODON_00002663 ['pork food product'] +FOODON_00002165 ['organ meat product'] +FOODON_00001048 ['meshanger cheese food product'] +FOODON_00001082 ['bitter cheese food product'] +FOODON_00001124 ['caprine cheese food product'] +FOODON_00001125 ['ovine cheese food product'] +FOODON_00001126 ['bovine cheese food product'] +FOODON_00001771 ['cow milk based food product'] +FOODON_00001216 ['cream food product'] +FOODON_00001067 ['buttermilk food product'] +FOODON_00001118 ['cattle dairy food product'] +FOODON_00001266 ['camel milk beverage'] +FOODON_00001114 ['zebra dairy food product'] +FOODON_00001291 ['clam food product'] +FOODON_00001292 ['oyster food product'] +FOODON_00001272 ['zebra milk beverage'] +FOODON_00001011 ['milk formula food product'] +FOODON_00001099 ['apple beverage'] +FOODON_00001210 ['wheat flour food product'] +FOODON_00001632 ['barley flour food product'] +FOODON_00001211 ['pasta food product'] +FOODON_00001193 ['fonio food product'] +FOODON_00001020 ['beer wort food product'] +FOODON_00001052 ['amasake food product'] +FOODON_00001060 ['awamori food product'] +FOODON_00001080 ['tape kefan food product'] +FOODON_00001064 ['bottled beer food product'] +FOODON_00001031 ['gorgonzola cheese food product'] +FOODON_00001129 ['goat milk cheese food product'] +FOODON_00001130 ['sheep milk cheese food product'] +FOODON_00001127 ['cow milk cheese'] +FOODON_00001075 ['mammalian milk (nonfat, dry)'] +FOODON_00001298 ['unpasteurized camel milk beverage'] +FOODON_00001040 ['chicken meat food product'] +FOODON_00001284 ['duck meat food product'] +FOODON_00001285 ['goose meat food product'] +FOODON_00001153 ['muskmelon (Cucumis melo) fruit food product'] +FOODON_00001021 ['acifified beer wort food product'] +FOODON_00001049 ['pork chop food product'] +FOODON_00001294 ['goat milk cheese (unpasteurized)'] +FOODON_00001296 ['sheep milk cheese (unpasteurized)'] +FOODON_00001025 ['camembert cheese food product'] +FOODON_00001027 ['cheddar cheese food product'] +FOODON_00001028 ['Brie cheese food product'] +FOODON_00001029 ['gouda cheese food product'] +FOODON_00001032 ['swiss cheese food product'] +FOODON_00001033 ['emmenthal cheese food product'] +FOODON_00001036 ['pont ieveque cheese food product'] +FOODON_00002252 ['soft cheese food product'] +FOODON_00001081 ['Bondon cheese food product'] +FOODON_00001035 ['new zealand cheddar cheese food product'] +FOODON_00001037 ['vacherin mont dor cheese food product'] diff --git a/local/.gitkeep b/local/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/nmdc_ontology/mixs_environments_extensions_to_envo_envirnmental_materials_by_claude.py b/nmdc_ontology/mixs_environments_extensions_to_envo_envirnmental_materials_by_claude.py new file mode 100644 index 0000000..8e9bada --- /dev/null +++ b/nmdc_ontology/mixs_environments_extensions_to_envo_envirnmental_materials_by_claude.py @@ -0,0 +1,44 @@ +import os +import time + +from anthropic import Anthropic + +# Set up the Anthropic API client +api_key = os.environ["ANTHROPIC_API_KEY"] +MODEL_NAME = "claude-3-opus-20240229" + +client = Anthropic(api_key=api_key) + +with open('../assets/extension_report.yaml', 'r') as file: + mixs_environments = file.read() + +with open('../assets/report_envo_environmental_material_annotations.tsv', 'r') as file: + envo_materials = file.read() + +def get_completion(client, prompt): + while True: + try: + return client.messages.create( + model=MODEL_NAME, + max_tokens=4096, + temperature=0.1, # 0 to 1 + messages=[{ + "role": 'user', "content": prompt + }] + ).content[0].text + except Exception as e: + print(f"{e}. Retrying in 5 seconds...") + time.sleep(5) + + + +completion = get_completion(client, + f"""Here are the definitions of environments, according to MIxS: {mixs_environments} +and the definitions of environmental materials, according to EnvO: {envo_materials}. +Generate an exhasutive YAML-formatted report of all environmental materials that could reasonalby be found in the Soil environment. +When associating an environmental material with an environment, +report both the environmental material id and the environmental material label for every associated environmental material. +""" +) + +print(completion) diff --git a/poetry.lock b/poetry.lock index c47c2d8..a2327b2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -26,6 +26,30 @@ files = [ {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, ] +[[package]] +name = "anthropic" +version = "0.21.1" +description = "The official Python library for the anthropic API" +optional = false +python-versions = ">=3.7" +files = [ + {file = "anthropic-0.21.1-py3-none-any.whl", hash = "sha256:31f9216221c60494089267fa60e8d50bed34b4e8bc7d691c9212967be08b952a"}, + {file = "anthropic-0.21.1.tar.gz", hash = "sha256:821fdbe3e65f1d1089f58646c0f724aff15e584942c15d8f7d60f09ecccc6e62"}, +] + +[package.dependencies] +anyio = ">=3.5.0,<5" +distro = ">=1.7.0,<2" +httpx = ">=0.23.0,<1" +pydantic = ">=1.9.0,<3" +sniffio = "*" +tokenizers = ">=0.13.0" +typing-extensions = ">=4.7,<5" + +[package.extras] +bedrock = ["boto3 (>=1.28.57)", "botocore (>=1.31.57)"] +vertex = ["google-auth (>=2,<3)"] + [[package]] name = "antlr4-python3-runtime" version = "4.9.3" @@ -36,6 +60,28 @@ files = [ {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, ] +[[package]] +name = "anyio" +version = "4.3.0" +description = "High level compatibility layer for multiple asynchronous event loop implementations" +optional = false +python-versions = ">=3.8" +files = [ + {file = "anyio-4.3.0-py3-none-any.whl", hash = "sha256:048e05d0f6caeed70d731f3db756d35dcc1f35747c8c403364a8332c630441b8"}, + {file = "anyio-4.3.0.tar.gz", hash = "sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6"}, +] + +[package.dependencies] +exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} +idna = ">=2.8" +sniffio = ">=1.1" +typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} + +[package.extras] +doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] +trio = ["trio (>=0.23)"] + [[package]] name = "appdirs" version = "1.4.4" @@ -383,6 +429,17 @@ files = [ {file = "distlib-0.3.8.tar.gz", hash = "sha256:1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64"}, ] +[[package]] +name = "distro" +version = "1.9.0" +description = "Distro - an OS platform information API" +optional = false +python-versions = ">=3.6" +files = [ + {file = "distro-1.9.0-py3-none-any.whl", hash = "sha256:7bffd925d65168f85027d8da9af6bddab658135b840670a223589bc0c8ef02b2"}, + {file = "distro-1.9.0.tar.gz", hash = "sha256:2fa77c6fd8940f116ee1d6b94a2f90b13b5ea8d019b98bc8bafdcabcdd9bdbed"}, +] + [[package]] name = "editorconfig" version = "0.12.4" @@ -497,6 +554,41 @@ docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1 testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"] typing = ["typing-extensions (>=4.8)"] +[[package]] +name = "fsspec" +version = "2024.3.1" +description = "File-system specification" +optional = false +python-versions = ">=3.8" +files = [ + {file = "fsspec-2024.3.1-py3-none-any.whl", hash = "sha256:918d18d41bf73f0e2b261824baeb1b124bcf771767e3a26425cd7dec3332f512"}, + {file = "fsspec-2024.3.1.tar.gz", hash = "sha256:f39780e282d7d117ffb42bb96992f8a90795e4d0fb0f661a70ca39fe9c43ded9"}, +] + +[package.extras] +abfs = ["adlfs"] +adl = ["adlfs"] +arrow = ["pyarrow (>=1)"] +dask = ["dask", "distributed"] +devel = ["pytest", "pytest-cov"] +dropbox = ["dropbox", "dropboxdrivefs", "requests"] +full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "dask", "distributed", "dropbox", "dropboxdrivefs", "fusepy", "gcsfs", "libarchive-c", "ocifs", "panel", "paramiko", "pyarrow (>=1)", "pygit2", "requests", "s3fs", "smbprotocol", "tqdm"] +fuse = ["fusepy"] +gcs = ["gcsfs"] +git = ["pygit2"] +github = ["requests"] +gs = ["gcsfs"] +gui = ["panel"] +hdfs = ["pyarrow (>=1)"] +http = ["aiohttp (!=4.0.0a0,!=4.0.0a1)"] +libarchive = ["libarchive-c"] +oci = ["ocifs"] +s3 = ["s3fs"] +sftp = ["paramiko"] +smb = ["smbprotocol"] +ssh = ["paramiko"] +tqdm = ["tqdm"] + [[package]] name = "funowl" version = "0.2.3" @@ -604,6 +696,17 @@ files = [ docs = ["Sphinx", "furo"] test = ["objgraph", "psutil"] +[[package]] +name = "h11" +version = "0.14.0" +description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1" +optional = false +python-versions = ">=3.7" +files = [ + {file = "h11-0.14.0-py3-none-any.whl", hash = "sha256:e3fe4ac4b851c468cc8363d500db52c2ead036020723024a109d37346efaa761"}, + {file = "h11-0.14.0.tar.gz", hash = "sha256:8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d"}, +] + [[package]] name = "hbreader" version = "0.9.1" @@ -615,6 +718,84 @@ files = [ {file = "hbreader-0.9.1.tar.gz", hash = "sha256:d2c132f8ba6276d794c66224c3297cec25c8079d0a4cf019c061611e0a3b94fa"}, ] +[[package]] +name = "httpcore" +version = "1.0.4" +description = "A minimal low-level HTTP client." +optional = false +python-versions = ">=3.8" +files = [ + {file = "httpcore-1.0.4-py3-none-any.whl", hash = "sha256:ac418c1db41bade2ad53ae2f3834a3a0f5ae76b56cf5aa497d2d033384fc7d73"}, + {file = "httpcore-1.0.4.tar.gz", hash = "sha256:cb2839ccfcba0d2d3c1131d3c3e26dfc327326fbe7a5dc0dbfe9f6c9151bb022"}, +] + +[package.dependencies] +certifi = "*" +h11 = ">=0.13,<0.15" + +[package.extras] +asyncio = ["anyio (>=4.0,<5.0)"] +http2 = ["h2 (>=3,<5)"] +socks = ["socksio (==1.*)"] +trio = ["trio (>=0.22.0,<0.25.0)"] + +[[package]] +name = "httpx" +version = "0.27.0" +description = "The next generation HTTP client." +optional = false +python-versions = ">=3.8" +files = [ + {file = "httpx-0.27.0-py3-none-any.whl", hash = "sha256:71d5465162c13681bff01ad59b2cc68dd838ea1f10e51574bac27103f00c91a5"}, + {file = "httpx-0.27.0.tar.gz", hash = "sha256:a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5"}, +] + +[package.dependencies] +anyio = "*" +certifi = "*" +httpcore = "==1.*" +idna = "*" +sniffio = "*" + +[package.extras] +brotli = ["brotli", "brotlicffi"] +cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"] +http2 = ["h2 (>=3,<5)"] +socks = ["socksio (==1.*)"] + +[[package]] +name = "huggingface-hub" +version = "0.21.4" +description = "Client library to download and publish models, datasets and other repos on the huggingface.co hub" +optional = false +python-versions = ">=3.8.0" +files = [ + {file = "huggingface_hub-0.21.4-py3-none-any.whl", hash = "sha256:df37c2c37fc6c82163cdd8a67ede261687d80d1e262526d6c0ce73b6b3630a7b"}, + {file = "huggingface_hub-0.21.4.tar.gz", hash = "sha256:e1f4968c93726565a80edf6dc309763c7b546d0cfe79aa221206034d50155531"}, +] + +[package.dependencies] +filelock = "*" +fsspec = ">=2023.5.0" +packaging = ">=20.9" +pyyaml = ">=5.1" +requests = "*" +tqdm = ">=4.42.1" +typing-extensions = ">=3.7.4.3" + +[package.extras] +all = ["InquirerPy (==0.3.4)", "Jinja2", "Pillow", "aiohttp", "gradio", "jedi", "mypy (==1.5.1)", "numpy", "pydantic (>1.1,<2.0)", "pydantic (>1.1,<3.0)", "pytest", "pytest-asyncio", "pytest-cov", "pytest-env", "pytest-rerunfailures", "pytest-vcr", "pytest-xdist", "ruff (>=0.1.3)", "soundfile", "types-PyYAML", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "typing-extensions (>=4.8.0)", "urllib3 (<2.0)"] +cli = ["InquirerPy (==0.3.4)"] +dev = ["InquirerPy (==0.3.4)", "Jinja2", "Pillow", "aiohttp", "gradio", "jedi", "mypy (==1.5.1)", "numpy", "pydantic (>1.1,<2.0)", "pydantic (>1.1,<3.0)", "pytest", "pytest-asyncio", "pytest-cov", "pytest-env", "pytest-rerunfailures", "pytest-vcr", "pytest-xdist", "ruff (>=0.1.3)", "soundfile", "types-PyYAML", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "typing-extensions (>=4.8.0)", "urllib3 (<2.0)"] +fastai = ["fastai (>=2.4)", "fastcore (>=1.3.27)", "toml"] +hf-transfer = ["hf-transfer (>=0.1.4)"] +inference = ["aiohttp", "pydantic (>1.1,<2.0)", "pydantic (>1.1,<3.0)"] +quality = ["mypy (==1.5.1)", "ruff (>=0.1.3)"] +tensorflow = ["graphviz", "pydot", "tensorflow"] +testing = ["InquirerPy (==0.3.4)", "Jinja2", "Pillow", "aiohttp", "gradio", "jedi", "numpy", "pydantic (>1.1,<2.0)", "pydantic (>1.1,<3.0)", "pytest", "pytest-asyncio", "pytest-cov", "pytest-env", "pytest-rerunfailures", "pytest-vcr", "pytest-xdist", "soundfile", "urllib3 (<2.0)"] +torch = ["safetensors", "torch"] +typing = ["types-PyYAML", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "typing-extensions (>=4.8.0)"] + [[package]] name = "idna" version = "3.6" @@ -2549,6 +2730,17 @@ files = [ {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"}, ] +[[package]] +name = "sniffio" +version = "1.3.1" +description = "Sniff out which async library your code is running under" +optional = false +python-versions = ">=3.7" +files = [ + {file = "sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2"}, + {file = "sniffio-1.3.1.tar.gz", hash = "sha256:f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc"}, +] + [[package]] name = "sortedcontainers" version = "2.4.0" @@ -2748,6 +2940,133 @@ files = [ linkml-runtime = "*" mkdocs-mermaid2-plugin = ">=0.6.0,<0.7.0" +[[package]] +name = "tokenizers" +version = "0.15.2" +description = "" +optional = false +python-versions = ">=3.7" +files = [ + {file = "tokenizers-0.15.2-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:52f6130c9cbf70544287575a985bf44ae1bda2da7e8c24e97716080593638012"}, + {file = "tokenizers-0.15.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:054c1cc9c6d68f7ffa4e810b3d5131e0ba511b6e4be34157aa08ee54c2f8d9ee"}, + {file = "tokenizers-0.15.2-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:a9b9b070fdad06e347563b88c278995735292ded1132f8657084989a4c84a6d5"}, + {file = "tokenizers-0.15.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ea621a7eef4b70e1f7a4e84dd989ae3f0eeb50fc8690254eacc08acb623e82f1"}, + {file = "tokenizers-0.15.2-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:cf7fd9a5141634fa3aa8d6b7be362e6ae1b4cda60da81388fa533e0b552c98fd"}, + {file = "tokenizers-0.15.2-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:44f2a832cd0825295f7179eaf173381dc45230f9227ec4b44378322d900447c9"}, + {file = "tokenizers-0.15.2-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:8b9ec69247a23747669ec4b0ca10f8e3dfb3545d550258129bd62291aabe8605"}, + {file = "tokenizers-0.15.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:40b6a4c78da863ff26dbd5ad9a8ecc33d8a8d97b535172601cf00aee9d7ce9ce"}, + {file = "tokenizers-0.15.2-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:5ab2a4d21dcf76af60e05af8063138849eb1d6553a0d059f6534357bce8ba364"}, + {file = "tokenizers-0.15.2-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:a47acfac7e511f6bbfcf2d3fb8c26979c780a91e06fb5b9a43831b2c0153d024"}, + {file = "tokenizers-0.15.2-cp310-none-win32.whl", hash = "sha256:064ff87bb6acdbd693666de9a4b692add41308a2c0ec0770d6385737117215f2"}, + {file = "tokenizers-0.15.2-cp310-none-win_amd64.whl", hash = "sha256:3b919afe4df7eb6ac7cafd2bd14fb507d3f408db7a68c43117f579c984a73843"}, + {file = "tokenizers-0.15.2-cp311-cp311-macosx_10_12_x86_64.whl", hash = "sha256:89cd1cb93e4b12ff39bb2d626ad77e35209de9309a71e4d3d4672667b4b256e7"}, + {file = "tokenizers-0.15.2-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:cfed5c64e5be23d7ee0f0e98081a25c2a46b0b77ce99a4f0605b1ec43dd481fa"}, + {file = "tokenizers-0.15.2-cp311-cp311-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:a907d76dcfda37023ba203ab4ceeb21bc5683436ebefbd895a0841fd52f6f6f2"}, + {file = "tokenizers-0.15.2-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:20ea60479de6fc7b8ae756b4b097572372d7e4032e2521c1bbf3d90c90a99ff0"}, + {file = "tokenizers-0.15.2-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:48e2b9335be2bc0171df9281385c2ed06a15f5cf121c44094338306ab7b33f2c"}, + {file = "tokenizers-0.15.2-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:112a1dd436d2cc06e6ffdc0b06d55ac019a35a63afd26475205cb4b1bf0bfbff"}, + {file = "tokenizers-0.15.2-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:4620cca5c2817177ee8706f860364cc3a8845bc1e291aaf661fb899e5d1c45b0"}, + {file = "tokenizers-0.15.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ccd73a82751c523b3fc31ff8194702e4af4db21dc20e55b30ecc2079c5d43cb7"}, + {file = "tokenizers-0.15.2-cp311-cp311-musllinux_1_1_aarch64.whl", hash = "sha256:107089f135b4ae7817affe6264f8c7a5c5b4fd9a90f9439ed495f54fcea56fb4"}, + {file = "tokenizers-0.15.2-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:0ff110ecc57b7aa4a594396525a3451ad70988e517237fe91c540997c4e50e29"}, + {file = "tokenizers-0.15.2-cp311-none-win32.whl", hash = "sha256:6d76f00f5c32da36c61f41c58346a4fa7f0a61be02f4301fd30ad59834977cc3"}, + {file = "tokenizers-0.15.2-cp311-none-win_amd64.whl", hash = "sha256:cc90102ed17271cf0a1262babe5939e0134b3890345d11a19c3145184b706055"}, + {file = "tokenizers-0.15.2-cp312-cp312-macosx_10_12_x86_64.whl", hash = "sha256:f86593c18d2e6248e72fb91c77d413a815153b8ea4e31f7cd443bdf28e467670"}, + {file = "tokenizers-0.15.2-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:0774bccc6608eca23eb9d620196687c8b2360624619623cf4ba9dc9bd53e8b51"}, + {file = "tokenizers-0.15.2-cp312-cp312-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:d0222c5b7c9b26c0b4822a82f6a7011de0a9d3060e1da176f66274b70f846b98"}, + {file = "tokenizers-0.15.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:3835738be1de66624fff2f4f6f6684775da4e9c00bde053be7564cbf3545cc66"}, + {file = "tokenizers-0.15.2-cp312-cp312-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:0143e7d9dcd811855c1ce1ab9bf5d96d29bf5e528fd6c7824d0465741e8c10fd"}, + {file = "tokenizers-0.15.2-cp312-cp312-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:db35825f6d54215f6b6009a7ff3eedee0848c99a6271c870d2826fbbedf31a38"}, + {file = "tokenizers-0.15.2-cp312-cp312-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:3f5e64b0389a2be47091d8cc53c87859783b837ea1a06edd9d8e04004df55a5c"}, + {file = "tokenizers-0.15.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9e0480c452217edd35eca56fafe2029fb4d368b7c0475f8dfa3c5c9c400a7456"}, + {file = "tokenizers-0.15.2-cp312-cp312-musllinux_1_1_aarch64.whl", hash = "sha256:a33ab881c8fe70474980577e033d0bc9a27b7ab8272896e500708b212995d834"}, + {file = "tokenizers-0.15.2-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:a308a607ca9de2c64c1b9ba79ec9a403969715a1b8ba5f998a676826f1a7039d"}, + {file = "tokenizers-0.15.2-cp312-none-win32.whl", hash = "sha256:b8fcfa81bcb9447df582c5bc96a031e6df4da2a774b8080d4f02c0c16b42be0b"}, + {file = "tokenizers-0.15.2-cp312-none-win_amd64.whl", hash = "sha256:38d7ab43c6825abfc0b661d95f39c7f8af2449364f01d331f3b51c94dcff7221"}, + {file = "tokenizers-0.15.2-cp313-cp313-macosx_10_12_x86_64.whl", hash = "sha256:38bfb0204ff3246ca4d5e726e8cc8403bfc931090151e6eede54d0e0cf162ef0"}, + {file = "tokenizers-0.15.2-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:9c861d35e8286a53e06e9e28d030b5a05bcbf5ac9d7229e561e53c352a85b1fc"}, + {file = "tokenizers-0.15.2-cp313-cp313-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:936bf3842db5b2048eaa53dade907b1160f318e7c90c74bfab86f1e47720bdd6"}, + {file = "tokenizers-0.15.2-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:620beacc3373277700d0e27718aa8b25f7b383eb8001fba94ee00aeea1459d89"}, + {file = "tokenizers-0.15.2-cp313-cp313-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:2735ecbbf37e52db4ea970e539fd2d450d213517b77745114f92867f3fc246eb"}, + {file = "tokenizers-0.15.2-cp313-cp313-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:473c83c5e2359bb81b0b6fde870b41b2764fcdd36d997485e07e72cc3a62264a"}, + {file = "tokenizers-0.15.2-cp313-cp313-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:968fa1fb3c27398b28a4eca1cbd1e19355c4d3a6007f7398d48826bbe3a0f728"}, + {file = "tokenizers-0.15.2-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:865c60ae6eaebdde7da66191ee9b7db52e542ed8ee9d2c653b6d190a9351b980"}, + {file = "tokenizers-0.15.2-cp313-cp313-musllinux_1_1_aarch64.whl", hash = "sha256:7c0d8b52664ab2d4a8d6686eb5effc68b78608a9008f086a122a7b2996befbab"}, + {file = "tokenizers-0.15.2-cp313-cp313-musllinux_1_1_x86_64.whl", hash = "sha256:f33dfbdec3784093a9aebb3680d1f91336c56d86cc70ddf88708251da1fe9064"}, + {file = "tokenizers-0.15.2-cp37-cp37m-macosx_10_12_x86_64.whl", hash = "sha256:d44ba80988ff9424e33e0a49445072ac7029d8c0e1601ad25a0ca5f41ed0c1d6"}, + {file = "tokenizers-0.15.2-cp37-cp37m-macosx_11_0_arm64.whl", hash = "sha256:dce74266919b892f82b1b86025a613956ea0ea62a4843d4c4237be2c5498ed3a"}, + {file = "tokenizers-0.15.2-cp37-cp37m-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:0ef06b9707baeb98b316577acb04f4852239d856b93e9ec3a299622f6084e4be"}, + {file = "tokenizers-0.15.2-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c73e2e74bbb07910da0d37c326869f34113137b23eadad3fc00856e6b3d9930c"}, + {file = "tokenizers-0.15.2-cp37-cp37m-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:4eeb12daf02a59e29f578a865f55d87cd103ce62bd8a3a5874f8fdeaa82e336b"}, + {file = "tokenizers-0.15.2-cp37-cp37m-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:9ba9f6895af58487ca4f54e8a664a322f16c26bbb442effd01087eba391a719e"}, + {file = "tokenizers-0.15.2-cp37-cp37m-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:ccec77aa7150e38eec6878a493bf8c263ff1fa8a62404e16c6203c64c1f16a26"}, + {file = "tokenizers-0.15.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f3f40604f5042ff210ba82743dda2b6aa3e55aa12df4e9f2378ee01a17e2855e"}, + {file = "tokenizers-0.15.2-cp37-cp37m-musllinux_1_1_aarch64.whl", hash = "sha256:5645938a42d78c4885086767c70923abad047163d809c16da75d6b290cb30bbe"}, + {file = "tokenizers-0.15.2-cp37-cp37m-musllinux_1_1_x86_64.whl", hash = "sha256:05a77cbfebe28a61ab5c3891f9939cc24798b63fa236d84e5f29f3a85a200c00"}, + {file = "tokenizers-0.15.2-cp37-none-win32.whl", hash = "sha256:361abdc068e8afe9c5b818769a48624687fb6aaed49636ee39bec4e95e1a215b"}, + {file = "tokenizers-0.15.2-cp37-none-win_amd64.whl", hash = "sha256:7ef789f83eb0f9baeb4d09a86cd639c0a5518528f9992f38b28e819df397eb06"}, + {file = "tokenizers-0.15.2-cp38-cp38-macosx_10_12_x86_64.whl", hash = "sha256:4fe1f74a902bee74a3b25aff180fbfbf4f8b444ab37c4d496af7afd13a784ed2"}, + {file = "tokenizers-0.15.2-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:4c4b89038a684f40a6b15d6b09f49650ac64d951ad0f2a3ea9169687bbf2a8ba"}, + {file = "tokenizers-0.15.2-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:d05a1b06f986d41aed5f2de464c003004b2df8aaf66f2b7628254bcbfb72a438"}, + {file = "tokenizers-0.15.2-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:508711a108684111ec8af89d3a9e9e08755247eda27d0ba5e3c50e9da1600f6d"}, + {file = "tokenizers-0.15.2-cp38-cp38-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:daa348f02d15160cb35439098ac96e3a53bacf35885072611cd9e5be7d333daa"}, + {file = "tokenizers-0.15.2-cp38-cp38-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:494fdbe5932d3416de2a85fc2470b797e6f3226c12845cadf054dd906afd0442"}, + {file = "tokenizers-0.15.2-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:c2d60f5246f4da9373f75ff18d64c69cbf60c3bca597290cea01059c336d2470"}, + {file = "tokenizers-0.15.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:93268e788825f52de4c7bdcb6ebc1fcd4a5442c02e730faa9b6b08f23ead0e24"}, + {file = "tokenizers-0.15.2-cp38-cp38-musllinux_1_1_aarch64.whl", hash = "sha256:6fc7083ab404019fc9acafe78662c192673c1e696bd598d16dc005bd663a5cf9"}, + {file = "tokenizers-0.15.2-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:41e39b41e5531d6b2122a77532dbea60e171ef87a3820b5a3888daa847df4153"}, + {file = "tokenizers-0.15.2-cp38-none-win32.whl", hash = "sha256:06cd0487b1cbfabefb2cc52fbd6b1f8d4c37799bd6c6e1641281adaa6b2504a7"}, + {file = "tokenizers-0.15.2-cp38-none-win_amd64.whl", hash = "sha256:5179c271aa5de9c71712e31cb5a79e436ecd0d7532a408fa42a8dbfa4bc23fd9"}, + {file = "tokenizers-0.15.2-cp39-cp39-macosx_10_12_x86_64.whl", hash = "sha256:82f8652a74cc107052328b87ea8b34291c0f55b96d8fb261b3880216a9f9e48e"}, + {file = "tokenizers-0.15.2-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:02458bee6f5f3139f1ebbb6d042b283af712c0981f5bc50edf771d6b762d5e4f"}, + {file = "tokenizers-0.15.2-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:c9a09cd26cca2e1c349f91aa665309ddb48d71636370749414fbf67bc83c5343"}, + {file = "tokenizers-0.15.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:158be8ea8554e5ed69acc1ce3fbb23a06060bd4bbb09029431ad6b9a466a7121"}, + {file = "tokenizers-0.15.2-cp39-cp39-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:1ddba9a2b0c8c81633eca0bb2e1aa5b3a15362b1277f1ae64176d0f6eba78ab1"}, + {file = "tokenizers-0.15.2-cp39-cp39-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:3ef5dd1d39797044642dbe53eb2bc56435308432e9c7907728da74c69ee2adca"}, + {file = "tokenizers-0.15.2-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:454c203164e07a860dbeb3b1f4a733be52b0edbb4dd2e5bd75023ffa8b49403a"}, + {file = "tokenizers-0.15.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0cf6b7f1d4dc59af960e6ffdc4faffe6460bbfa8dce27a58bf75755ffdb2526d"}, + {file = "tokenizers-0.15.2-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:2ef09bbc16519f6c25d0c7fc0c6a33a6f62923e263c9d7cca4e58b8c61572afb"}, + {file = "tokenizers-0.15.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:c9a2ebdd2ad4ec7a68e7615086e633857c85e2f18025bd05d2a4399e6c5f7169"}, + {file = "tokenizers-0.15.2-cp39-none-win32.whl", hash = "sha256:918fbb0eab96fe08e72a8c2b5461e9cce95585d82a58688e7f01c2bd546c79d0"}, + {file = "tokenizers-0.15.2-cp39-none-win_amd64.whl", hash = "sha256:524e60da0135e106b254bd71f0659be9f89d83f006ea9093ce4d1fab498c6d0d"}, + {file = "tokenizers-0.15.2-pp310-pypy310_pp73-macosx_10_12_x86_64.whl", hash = "sha256:6a9b648a58281c4672212fab04e60648fde574877d0139cd4b4f93fe28ca8944"}, + {file = "tokenizers-0.15.2-pp310-pypy310_pp73-macosx_11_0_arm64.whl", hash = "sha256:7c7d18b733be6bbca8a55084027f7be428c947ddf871c500ee603e375013ffba"}, + {file = "tokenizers-0.15.2-pp310-pypy310_pp73-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:13ca3611de8d9ddfbc4dc39ef54ab1d2d4aaa114ac8727dfdc6a6ec4be017378"}, + {file = "tokenizers-0.15.2-pp310-pypy310_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:237d1bf3361cf2e6463e6c140628e6406766e8b27274f5fcc62c747ae3c6f094"}, + {file = "tokenizers-0.15.2-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:67a0fe1e49e60c664915e9fb6b0cb19bac082ab1f309188230e4b2920230edb3"}, + {file = "tokenizers-0.15.2-pp310-pypy310_pp73-musllinux_1_1_aarch64.whl", hash = "sha256:4e022fe65e99230b8fd89ebdfea138c24421f91c1a4f4781a8f5016fd5cdfb4d"}, + {file = "tokenizers-0.15.2-pp310-pypy310_pp73-musllinux_1_1_x86_64.whl", hash = "sha256:d857be2df69763362ac699f8b251a8cd3fac9d21893de129bc788f8baaef2693"}, + {file = "tokenizers-0.15.2-pp37-pypy37_pp73-macosx_10_12_x86_64.whl", hash = "sha256:708bb3e4283177236309e698da5fcd0879ce8fd37457d7c266d16b550bcbbd18"}, + {file = "tokenizers-0.15.2-pp37-pypy37_pp73-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:64c35e09e9899b72a76e762f9854e8750213f67567787d45f37ce06daf57ca78"}, + {file = "tokenizers-0.15.2-pp37-pypy37_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c1257f4394be0d3b00de8c9e840ca5601d0a4a8438361ce9c2b05c7d25f6057b"}, + {file = "tokenizers-0.15.2-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:02272fe48280e0293a04245ca5d919b2c94a48b408b55e858feae9618138aeda"}, + {file = "tokenizers-0.15.2-pp37-pypy37_pp73-musllinux_1_1_aarch64.whl", hash = "sha256:dc3ad9ebc76eabe8b1d7c04d38be884b8f9d60c0cdc09b0aa4e3bcf746de0388"}, + {file = "tokenizers-0.15.2-pp37-pypy37_pp73-musllinux_1_1_x86_64.whl", hash = "sha256:32e16bdeffa7c4f46bf2152172ca511808b952701d13e7c18833c0b73cb5c23f"}, + {file = "tokenizers-0.15.2-pp38-pypy38_pp73-macosx_10_12_x86_64.whl", hash = "sha256:fb16ba563d59003028b678d2361a27f7e4ae0ab29c7a80690efa20d829c81fdb"}, + {file = "tokenizers-0.15.2-pp38-pypy38_pp73-macosx_11_0_arm64.whl", hash = "sha256:2277c36d2d6cdb7876c274547921a42425b6810d38354327dd65a8009acf870c"}, + {file = "tokenizers-0.15.2-pp38-pypy38_pp73-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:1cf75d32e8d250781940d07f7eece253f2fe9ecdb1dc7ba6e3833fa17b82fcbc"}, + {file = "tokenizers-0.15.2-pp38-pypy38_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f1b3b31884dc8e9b21508bb76da80ebf7308fdb947a17affce815665d5c4d028"}, + {file = "tokenizers-0.15.2-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b10122d8d8e30afb43bb1fe21a3619f62c3e2574bff2699cf8af8b0b6c5dc4a3"}, + {file = "tokenizers-0.15.2-pp38-pypy38_pp73-musllinux_1_1_aarch64.whl", hash = "sha256:d88b96ff0fe8e91f6ef01ba50b0d71db5017fa4e3b1d99681cec89a85faf7bf7"}, + {file = "tokenizers-0.15.2-pp38-pypy38_pp73-musllinux_1_1_x86_64.whl", hash = "sha256:37aaec5a52e959892870a7c47cef80c53797c0db9149d458460f4f31e2fb250e"}, + {file = "tokenizers-0.15.2-pp39-pypy39_pp73-macosx_10_12_x86_64.whl", hash = "sha256:e2ea752f2b0fe96eb6e2f3adbbf4d72aaa1272079b0dfa1145507bd6a5d537e6"}, + {file = "tokenizers-0.15.2-pp39-pypy39_pp73-macosx_11_0_arm64.whl", hash = "sha256:4b19a808d8799fda23504a5cd31d2f58e6f52f140380082b352f877017d6342b"}, + {file = "tokenizers-0.15.2-pp39-pypy39_pp73-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:64c86e5e068ac8b19204419ed8ca90f9d25db20578f5881e337d203b314f4104"}, + {file = "tokenizers-0.15.2-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:de19c4dc503c612847edf833c82e9f73cd79926a384af9d801dcf93f110cea4e"}, + {file = "tokenizers-0.15.2-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ea09acd2fe3324174063d61ad620dec3bcf042b495515f27f638270a7d466e8b"}, + {file = "tokenizers-0.15.2-pp39-pypy39_pp73-musllinux_1_1_aarch64.whl", hash = "sha256:cf27fd43472e07b57cf420eee1e814549203d56de00b5af8659cb99885472f1f"}, + {file = "tokenizers-0.15.2-pp39-pypy39_pp73-musllinux_1_1_x86_64.whl", hash = "sha256:7ca22bd897537a0080521445d91a58886c8c04084a6a19e6c78c586e0cfa92a5"}, + {file = "tokenizers-0.15.2.tar.gz", hash = "sha256:e6e9c6e019dd5484be5beafc775ae6c925f4c69a3487040ed09b45e13df2cb91"}, +] + +[package.dependencies] +huggingface_hub = ">=0.16.4,<1.0" + +[package.extras] +dev = ["tokenizers[testing]"] +docs = ["setuptools_rust", "sphinx", "sphinx_rtd_theme"] +testing = ["black (==22.3)", "datasets", "numpy", "pytest", "requests"] + [[package]] name = "tomli" version = "2.0.1" @@ -3024,4 +3343,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "d5b07e3d2be4cfc92e022645e253397c355f130adf0ab0924e9c5728c99f7126" +content-hash = "d9441720a39010428ac0167bf8b24a47dea68d8d222367827807c55a0ca50ebb" diff --git a/pyproject.toml b/pyproject.toml index dda33a9..ad5bcf8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,6 +10,7 @@ readme = "README.md" python = "^3.10" oaklib = "^0.5.25" pyarrow = "^15.0.0" +anthropic = "^0.21.1" [build-system] requires = ["poetry-core"]