https://creativecommons.org/licenses/by-nc-sa/4.0/ Birgitta König-Ries birgitta.koenig-ries@uni-jena.de https://creativecommons.org/licenses/by-nc-sa/4.0/ Invasion Biology Ontology Hrishikesh Jadhav jadhav02@ads.uni-passau.de Alsayed Algergawy alsayed.algergawy@uni-jena.de Merle Gänßinger merle.gaenssinger@uni-jena.de Tina Heger t.heger@tum.de https://creativecommons.org/licenses/by-nc-sa/4.0/ https://creativecommons.org/licenses/by-nc-sa/4.0/ The Invasion Biology Ontology (INBIO) contains terms and concepts relevant in the field of invasion biology, which is a research area dealing with the translocation, establishment, spread, impact and management of species outside of their native ranges, where they are called non-native or alien species. This first version of the ontology covers terms and concepts needed to describe twelve major invasion hypotheses building the hierarchical hypothesis network (see also Jeschke JM, Heger T (Eds) (2018) Invasion Biology: Hypotheses and Evidence. CABI, Wallingford, UK). 1.1 1.2 license GROUP:OBI:<http://purl.obfoundry.org/obo/obi> PERSON:Daniel Schober editor note contributor An entity responsible for making contributions to the resource. license title license license created by influences affects decreases has component has distribution has growth has mortality has natality has number of individuals has recruitment increases is affected by is characteristic of is characterized by is growth of is habitat of is mortality of is natality of is part of is recruitment of is status of The characteristicFor property gives the entity of the characteristic. http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#characteristicFor characteristic for The hasMeasurement property gives the measurements of the observed entity. http://ecoinformatics.org/oboe/oboe.1.1/oboe-core.owl#hasMeasurement has measurement Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of a core relation that holds between a part and its whole http://purl.obolibrary.org/obo/omrse.owl aggregate of is aggregate of Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) BFO2 Reference: independent continuant BFO2 Reference: spatial region occupies spatial region at occupies spatial region at some time b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002]) if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001]) [copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region has spatial occupant at some time [copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) has measurement unit label A relation between a value specification and its unit of measurement. http://purl.obolibrary.org/obo/obi.owl has measurement unit label this input material (or this output material) participates in this process http://purl.obolibrary.org/obo/obi.owl participates in a relation between a continuant and a process, in which the continuant is somehow involved in the process this red color is a quality of this apple A quality inheres in its bearer at all times for which the quality exists. is quality of quality of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives into a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime is location of location of a relation between two independent continuants, the location and the target, in which the target is entirely within the location Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained in contains This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. David Osumi-Sutherland overlaps ends during Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". capable of A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall surrounds Chris Mungall finished by ends with has habitat We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to Chris Mungall In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to Chris Mungall enabled by Chris Mungall This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with https://github.com/oborel/obo-relations/wiki/InteractionRelations Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall in pairwise interaction with Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. interacts with http://purl.obolibrary.org/obo/MI_0914 A relationship that holds between two entities in which the processes executed by the two entities are causally connected. gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of Melissa Haendel Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces Melissa Haendel produced by is absent facilitate has increased effort level by completed invasion phase has index is native range to has status has range is in invasion phase increases effort in has level of decreases effort in is closely related to Two species are closely related if they split apart from each other relatively recently during their evolution.. enemy in sense of http://www.semanticweb.org/rs/ontologies/INBIO#enemy is enemy of has decreased effort level by is enhanced by enhance is range of achieves alien range: range in which the species is not commonly found has alien range allocates has area has propagule pressure shows changes in species trait is prey of has value is similar to is alien range to is against has role native range: range in which the species is commonly found has native range General influence or effect on ecological or biological systems. affects Conducts a detailed examination of the elements or structure of something. analyzes Refers to the process of pushing out or replacing one species or ecological component by another. displaces Interrupts by causing a disturbance or problem. disrupts Causes or motivates a change or process. drives Improves or augments a particular ecological or biological property or process. enhances Studies or investigates a subject or area in detail. examines Indicates undergoing or being subjected to a particular process or condition. experiences Makes an action or process easy or easier. facilitates Acts as a host for other organisms, often referring to invasive species. hosts Describes significant effects on ecosystems or species. impacts Influences biological or ecological processes. influences Makes available for use; supplies. provides Measures or expresses as a quantity. quantifies Decreases in size, number, or extent. reduces A relation between a scalar measurement data item and a number that quantifies it. The range should probably not be restricted to "float". It makes sense to set it to "real". However we do not know how this change will affect SPARQL queries, so we have left the range as-is for now. http://purl.obolibrary.org/obo/obi.owl has measurement value define range 0 to 1 has invasion success likelihood has amount of species has amount of closely related species has specific name ccon:Biodiversity It's the degree of veriation of life forms within a given species, ecosystem, biome, or planet. Source: wikipedia.org biodiversity biological diversity The biological variation found in a defined spatial area: can refer to variation at the level of genome, phenotype, species, community or ecosystem. ccon:ComunityDynamics The community dynamics is the study of changes over time of the structure of biological communities. community dynamics ccon:Difference It's the difference of any parameter (size, number of deads, number of recruits etc.) between two dates. difference ccon:DiversityIndex It's a quantitative measure that reflects how many different types (such as species) there are in a dataset, and can simultaneously takes into account how evenly the basic units (such as individuals) are distributed among those types. Source: wikipedia.org diversity index ccon:FireIncidence The occurrence of burning in ecosystems. fire incidence ccon:GeographicalDistribution geographical distribution A geographical region that can include land as well as water. <_000133>update definition ccon:GrowthRate It's a measure of the changes in population or community size over time. growth growth rate ccon:Mortality It's the number of individuals dead over time. death rate mortality mortality rate ccon:PielousEvennessIndex It's a representation of the evenness and quantifies how equal the community is numerically. pielou's evenness index ccon:Precipitation Any product of the condensation of atmospheric water vapour that falls under gravity (http://en.wikipedia.org/wiki/Precipitation) Qualquer produto da condensação do vapor de água atmosférico que cai sob efeito da gravidade. average annual precipitation precipitation rainfall ccon:Recruitment It's the rate on which new individuals establishes in a certain community either by new born individuals or immigration. recruitment recruitment rate ccon:RelativeHumidity Quantidade relativa de vapor de água na atmosfera The relative amount of whater vapour in the atmosphere mean annual relative humidity relative humidity ccon:SimpsonsIndex The simplest measure of the character of a community that takes into account both the abundance (or biomass) patterns and the species richness (Begon et al., 2006). simpson's index ccon:SorensensSimilarityIndex Sørensen–dice index Sørensen’s similarity coefficient sorensen's similarity index ccon:SpeciesEvenness Evenness is simply a measure of how similar specie are in their abundances. species evenness ccon:SpeciesRichness the number of differnet species represented in an ecological community, landscape or region species richness ccon:Temperature It is a measure of the thermal energy per particle of matter or radiation; it is measured by a thermometer, which may be calibrated in any of various temperature scales, Celsius, Fahrenheit, Kelvin, etc (http://en.wikipedia.org/wiki/Temperature). mean annual temperature temperature ccon:shannonsDiversityIndex shannon's diversity index BFO:0000002 BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants continuant A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) BFO:0000004 a spatial region an organism independent continuant A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) BFO:0000020 specifically dependent continuant A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. BFO:0000029 site BFO:0000031 generically dependent continuant A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. BFO:0000040 a hurricane a puff of smoke a sea wave a tornado BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. material material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) CHEBI:15377 water ENVO:00000000 https://en.wikipedia.org/wiki/Geographic_feature macroscopic spatial feature envoPolar May appear on a map. geographic feature ENVO:00000002 FTT:78 TGN:50001 man-made feature manmade feature anthropogenic geographic feature An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature. ENVO:00000012 FTT:131 FTT:280 FTT:711 FTT:761 FTT:824 FTT:825 FTT:826 FTT:827 FTT:828 FTT:829 Geonames:H.OVF fluvial feature envoPolar hydrographic feature A geographical feature associated with water. fluvial feature ADL:FTT ENVO:00000015 LTER:695 EcoLexicon:ocean FTT:1019 FTT:943 Geonames:H.OCN SWEETRealm:Ocean TGN:21102 https://en.wikipedia.org/wiki/Ocean ocean region envoMarine envoPolar ocean A marine water body which is constitutes the majority of an astronomical body's hydrosphere. LTER:695 http://129.24.124.196/vocab/vocab/index.php?tema=127&/coral-reefs ocean region ADL:FTT EcoLexicon:sea FTT:233 FTT:830 Geonames:H.SEA TGN:21103 https://en.wikipedia.org/wiki/Sea channel closed sea marginal sea open sea open sound open water ENVO ENVO:00000016 envoMarine envoPolar sea A large expanse of saline water usually connected with an ocean. ENVO:00000016 closed sea USGS:SDTS marginal sea USGS:SDTS open sea USGS:SDTS open sound USGS:SDTS open water USGS:SDTS ENVO ENVO:00000017 saline hydrographic feature A geographical feature associated with water with a halinity above 30 ppt (roughly 35 g/L). ENVO:00000017 ENVO:00000019 FTT:221 FTT:907 Geonames:H.LKN Geonames:H.LKSN TGN:21116 https://en.wikipedia.org/wiki/Saline_lake salt lake salina soda lake saline lake A lake whose water contains a considerable concentration of dissolved salts. salt lake USGS:SDTS salina USGS:SDTS ENVO:00000020 LTER:278 EcoLexicon:lake FTT:221 FTT:704 FTT:909 Geonames:H.LK Geonames:H.LKS SPIRE:Lake_or_pond SWEETRealm:Lake TGN:21114 TGN:21115 catch basin open water tarn broad llyn loch lochan lough mere mortlake pasteuer lake envoPolar lake A body of water or other liquid of considerable size contained in a depression on a landmass. LTER:278 http://129.24.124.196/vocab/vocab/index.php?tema=278&/lakes catch basin USGS:SDTS open water USGS:SDTS tarn ADL:FTT lochan ADL:FTT mortlake USGS:SDTS pasteuer lake USGS:SDTS ENVO:00000043 wetland region wetland area An vegetated area which overlaps a wetland ecosystem. wetland region NASA:earthrealm ENVO:00000045 LTER:182 mouth EcoLexicon:estuary FTT:234 Geonames:H.ESTY SWEETRealm:Estuary TGN:21152 https://en.wikipedia.org/wiki/Estuary inlet estuary A semi-enclosed coastal body of water with one or more rivers or streams flowing into it, and with a free connection to the open sea. LTER:182 https://vocab.lternet.edu/vocab/vocab/index.php?tema=182&/estuaries mouth USGS:SDTS inlet USGS:SDTS ENVO:00000063 hydrographic feature EcoLexicon:waterbody FTT:131 FTT:280 FTT:827 SWEETRealm:BodyOfWater TGN:21100 TGN:21101 https://en.wikipedia.org/wiki/Water_body aquatic feature bodies of water waterbody https://en.wikipedia.org/wiki/ The term body of water most often refers to large accumulations of water, such as oceans, seas, and lakes, but it includes smaller pools of water such as ponds, wetlands, or more rarely, puddles. A body of water does not have to be still or contained; Rivers, streams, canals, and other geographical features where water moves from one place to another are also considered bodies of water. body of water water body An accumulation of water of varying size. hydrographic feature ADL:FTT bodies of water Getty:TGN ENVO:00000131 EcoLexicon:ice FTT:648 SWEETRealm:LandIce TGN:21410 glacer Ice LandIce glacial landform glacier feature envoPolar Likely to be depopulated and "glacial" made into a quality or similar. glacial feature A hydrographic feature characterized by the dominance of snow or ice. glacer ADL:FTT Ice NASA:earthrealm LandIce NASA:earthrealm glacial landform Getty:TGN glacier feature ADL:FTT ENVO:00000134 EcoLexicon:permafrost LTER:408 https://en.wikipedia.org/wiki/Permafrost Permafrost envoPolar 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 Soil or rock and included ice or organic material at or below the freezing point of water (0 degrees Celsius or 32 degrees Fahrenheit) for two or more years. Permafrost NASA:earthrealm ENVO:00000228 inverse estuary An estuary which is located in regions where evaporation greatly exceeds the inflow of fresh water, forming a zone of maximum salinity towards which both riverine and marine water masses flow, before sinking and spreading along the bottom in both seaward and landward directions. ENVO ENVO:00000240 It would be more correct to say that this has_quality salty or has_part ((soil and water) and has_increased_levels_of salt. saline wetland ENVO:00000240 ENVO:00000304 coastal zone EcoLexicon:shore FTT:240 FTT:503 FTT:504 Geonames:T.SHOR SWEETRealm:Shore TGN:21481 https://en.wikipedia.org/wiki/Shore shoreface beach face foreshore inshore rivage seashore strand shore That part of the land in immediate contact with a body of water including the area between high and low water lines. strand USGS:SDTS coastal zone ADL:FTT shoreface USGS:SDTS beach face USGS:SDTS foreshore USGS:SDTS inshore USGS:SDTS rivage USGS:SDTS seashore USGS:SDTS EcoLexicon:rock FTT:1010 FTT:145 Geonames:T.RK Geonames:T.RKS SWEETRealm:Rock TGN:21444 https://en.wikipedia.org/wiki/Rock ENVO ENVO:00001995 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 A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids. ENVO:00001995 ENVO:00001998 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 LTER:535 SPIRE:Soil SWEETRealm:Soil https://en.wikipedia.org/wiki/Soil '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 " 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. The 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 Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. ENVO:00002005 EcoLexicon:air LTER:18 SWEETRealm:Air https://en.wikipedia.org/wiki/Air envoPolar air 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. ENVO:00002006 water EcoLexicon:water LTER:617 https://en.wikipedia.org/wiki/Water liquid water An environmental material primarily composed of dihydrogen oxide in its liquid form. ENVO:00002007 EcoLexicon:sediment EcoLexicon:sedimentation LTER:492 LTER:493 SWEETRealm:Sediment https://en.wikipedia.org/wiki/Sediment envoPolar It is recommended to use a combination of sediment terms to describe a more specific sediment type. sediment Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid. ENVO ENVO:00002297 A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. environmental feature A material entity which determines an environmental system. ENVO:00002297 ENVO:00002982 EcoLexicon:clay SWEETRealm:Clay https://en.wikipedia.org/wiki/Clay clay A group of hydrous aluminium phyllosilicate (phyllosilicates being a subgroup of silicate minerals) minerals (see clay minerals), that are typically less than 2 micrometres in diameter. Clay consists of a variety of phyllosilicate minerals rich in silicon and aluminium oxides and hydroxides which include variable amounts of structural water. ENVO ENVO:00003082 This could be demoted to an inferred class if issues with double inheritance arise. enriched soil A portion of enriched soil is a portion of soil with elevated levels of some material entity. ENVO:00003082 ENVO:00010483 portion of environmental material Everything under this parent must be a mass noun. 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". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. environmental material A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. ENVO:00010504 EcoLexicon:surface http://sweetontology.net/reprSpaceGeometry/Surface https://en.wikipedia.org/wiki/Surface This class is distinct from a geometric surface, which is two-dimensional. The idea of "uppermost" may be problematic. Further, the definition of layer (the superclass of surface in rev 133) references surface. This may be another issue. Perhaps this can be made into an inferred class using 'bounding layer of' some material entity, note that 'bounding layer' implies containment, which may not be valid here. surface layer A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings. ENVO:01000016 EcoLexicon:silt SWEETRealm:Silt https://en.wikipedia.org/wiki/Silt https://en.wikipedia.org/wiki/ 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 Silt is granular material of a size somewhere between sand and clay whose mineral origin is quartz and feldspar. EcoLexicon:sand LTER:484 SWEETRealm:Sand https://en.wikipedia.org/wiki/Sand ENVO ENVO:01000017 sand A naturally occurring granular material composed of finely divided rock and mineral particles. ENVO:01000017 ENVO:01000044 ORCID:0000-0002-4366-3088 envoPolar marine pelagic feature A prominent or distinctive aspect, quality, or characteristic of environments occurring within the marine water column. ENVO:01000060 Subclasses should be assigned by inference. envoAtmo envoPolar particulate matter Particulate material is an environmental material which is composed of microscopic portions of solid or liquid material suspended in another environmental material. ENVO:01000155 ORCID:0000-0002-4366-3088 EcoLexicon:organic_material biomass organic material Environmental material derived from living organisms and composed primarily of one or more biomacromolecules. ORCID:0000-0002-4366-3088 pbuttigi envrionmental characteristic ENVO ENVO:01000203 envoPolar A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional. An abiotic environmental factor that influences the functioning of living organisms (Begon et al., 2006). Experimental class created in EnvO. A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional. environmental condition An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system. ENVO:01000203 ENVO:01000254 EcoLexicon:environment environment In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. The environment of an organism consists of all those factors and phenomena outside the organism that influence it, whether these are physical and chemical (abiotic) or other organisms (biotic) (Begon et al., 2006) environmental system A system which has the disposition to environ one or more material entities. ENVO:01000256 Look for "mineral" in a chemical or geochemical ontology to formalise the composed primarily of link. 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. ORCID:0000-0002-4366-3088 LTER:341 mineral material 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. ORCID:0000-0002-4366-3088 aqueous vapor aqueous vapour ENVO ENVO:01000266 Perhaps a better relation between water vapour and water can be found in or added to RO? water vapour Water vapour is a vapour which is the gas phase of water. ENVO:01000266 aqueous vapor https://en.wikipedia.org/wiki/Water_vapor aqueous vapour https://en.wikipedia.org/wiki/Water_vapor ENVO:01000267 ORCID:0000-0002-4366-3088 LTER:48 atmosphere An atmosphere is a layer of gases surrounding a material body of sufficient mass that is held in place by the gravity of the body. ORCID:0000-0002-4366-3088 atmospheric water vapor ENVO ENVO:01000268 envoPolar atmospheric water vapour Atmospheric water vapour is water vapour that is part of an atmosphere. ENVO:01000268 atmospheric water vapor https://en.wikipedia.org/wiki/Water_vapor ENVO:01000276 ORCID:0000-0002-4366-3088 envoPolar Unlike biomes, ecoregions are geographically defined entities. ENVO's sister project, GAZ, contains terms for instances of ecoregions (e.g. Beringia lowland tundra). Requests for new terms should be directed to GAZ. ENVO will only contain this top-level class. The class' definition is preliminary and will be aligned to BFO. ecoregion A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions. ENVO:01000277 ORCID:0000-0002-4366-3088 LTER:262 ice envoPolar water ice Ice is water frozen into a solid state. It 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. ice http://www.eionet.europa.eu/gemet/concept/4131 ENVO:01000280 ORCID:0000-0002-4366-3088 envoPolar ENVO contains this top-level class, but all instances will be in GAZ. The definition is preliminary and will be aligned to BFO. https://en.wikipedia.org/wiki/ Ecozones correspond to the floristic kingdoms of botany or zoogeographic regions of zoology. Ecozones are characterized by the evolutionary history of the organisms they contain. They are distinct from biomes, also known as major habitat types, which are divisions of the Earth's surface based on life form, or the adaptation of plants and animals to climatic, soil, and other conditions. Biomes are characterized by similar climax vegetation. Each ecozone may include a number of different biomes. A tropical moist broadleaf forest in Central America, for example, may be similar to one in New Guinea in its vegetation type and structure, climate, soils, etc., but these forests are inhabited by plants and animals with very different evolutionary histories. ecozone Ecozones delineate large areas of a planetary surface within which organisms have been evolving in relative isolation over long periods of time, separated from one another by geographic features, such as oceans, broad deserts, or high mountain ranges, that constitute barriers to migration. ENVO:01000281 ORCID:0000-0002-4366-3088 envoPolar Preliminary definition. layer A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface. ENVO:01000295 ORCID:0000-0002-4366-3088 envoMarine envoPolar marine layer A layer that is part of a marine water body. ENVO:01000303 endolithic environment An endolithic environment is an environment that exists within solid rock. ENVO:01000309 envoPolar The definition of the deprecated 'cold temperature habitat' class, which this class was derived from, quotes an upper threshold of 15 degrees Celsius for 'coldness'. cold environment An environment which has a lower temperature than some local or global average. ENVO:01000313 Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic. anthropogenic environment An anthropogenic environment is an environmental system which is the product of human activity. ENVO:01000314 high osmolarity environment true A high osmolarity environment is an environment in which entities are exposed to high concentrations of solutes. ENVO:01000317 aquatic environment An environment whose dynamics are strongly influenced by water. ENVO:01000320 envoPolar marine environment A marine environment and enviroment which is determined by a marine water body. ENVO:01000325 envoPolar This class will eventually be populated by inference, and its asserted subclasses removed. aquatic layer A layer in a water mass, itself composed primarily of water. ENVO:01000406 envoPolar snow Snow is an environmental material which is primarily composed of flakes of crystalline water ice. ENVO:01000408 environmental area envoPolar Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition. environmental zone A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein. ENVO:01000445 envoPolar This is often used by plant collectors when early successional species are observed in an area. disturbed ecosystem An ecosystem which has been subject to a perturbation, that is, the ecosystem has undergone a pronounced change in response to a change in environmental conditions or other perturbation. ENVO:01000624 condensation envoPolar "process" is included in the label to make it clear that we are not referring to the condensed material (e.g. water droplets, window fog) hydrological condensation process Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase. ENVO:01000687 Used for both marine and lake coasts. The boundary of the coast is fuzzy and it overlaps both the water body and land in quesiton. Compared to 'shore' coast A coast is the area where land meets the sea, ocean, or lake. ENVO:01000703 precipitation "process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet) hydrological precipitation process Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity. ENVO:01000724 condensation process Condensation is a process during which a gas undergoes a phase transition into a liquid. ENVO:01000739 EcoLexicon:habitat LTER:238 SWEETRealm:Habitat https://en.wikipedia.org/wiki/Habitat A habitat's specificity to an ecological population differentiates it from other environment classes. habitat An environmental system which can sustain and allow the growth of an ecological population. ENVO:01000797 This class is to be populated by inference. gas gaseous environmental material A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely. ENVO:01000814 This is a defined class: its subclasses will not be asserted, but filled by inference. solid environmental material An environmental material which is in a solid state. ENVO:01000815 envoPolar This is a defined class: its subclasses will not be asserted, but filled by inference. liquid environmental material An environmental material which is in a liquid state. ENVO:01000817 Whether this class should be grouped with classes such as "hydrosphere" and "cryosphere" requires some discussion. envoAstro envoPolar The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations. biosphere A biosphere is a part of an astronomical body which includes, as parts, all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact. A biosphere is an environmental system which includes, as parts, all the living entities within the gravitational sphere of influence of an astronomical body, and the non-living and dead entities which they interact with. ENVO:01000818 envoAstro envoPolar This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class. cryosphere A cryosphere is that part of a planet which is primarily composed of water is in solid form. ENVO:01000875 precipitation process A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force. ENVO:01000895 snow fall environmental_hazards envoPolar snowfall A hydrological process in which irregular aggregates of snow fall to a planetary surface. ENVO:01000951 In most contexts, 'natural' is defined by the lack of intervention or influence by humans and their activities. On Earth, most environments fall on a scale between completely natural and anthropised. natural environment non-anthropized environment An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. ENVO:01000952 anthropization An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action. anthropisation A process during which a natural environmental system is altered by human action. An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action. https://en.wikipedia.org/wiki/Anthropization ENVO:01000981 envoPolar This class can refer to the flow of any material in a liquid phase. mass liquid flow A process whereby a volume of liquid moves due to a disequilibrium of physical forces. ENVO:01000982 environmental_hazards water flow process A process during which a volume of water is transported due to a disequilibria in physical forces. ENVO:01000997 Organisational class. Not intended for annotation. environmental system determined by a quality true An environmental system which is determined by materials bearing roughly homogeneous qualities. ENVO:01000998 Organisational class. Not intended for annotation. Subclasses describe environments which are usually permeated by an environmental material. They may also describe environments which are sufficiently close to a material, that their dynamics are strongly influenced by it (e.g. a patch of forest ecosystem neighbouring a uranium dump). environmental system determined by a material true An environmental system within which an environmental material strongly influences the system's composition and properties. ENVO:01001000 host-associated environment envoEmpo envoOmics environmental system determined by an organism An environmental system which is determined by a living organism. ENVO:01001002 animal environment Metazoan-associated environment envoEmpo envoMeo envoOmics animal-associated environment An environmental system determined by an animal. ENVO:01001022 This class is to be filled by inference. natural lake A lake which has formed as the result of processes that are not or are only minimally driven by human activity. ENVO:01001023 Requires addition of waves for full axiomatisation. This should be linked to "subatomic particle" with an "or". Note that ENVO represents space as an environmental material (a hard vacuum with sparse material inclusions). environmental_hazards envoAstro radiation A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium. ENVO:01001040 envoEmpo The thresholds for "significant" concentrations of salts vary widely and thus no committment is made in this class. Subclasses with more explicit thresholds can be made upon request. saline environment An environment which is determined by materials which bear significant concentrations of salts. ENVO:01001044 envoEmpo envoOmics soil environment An environmental system which has its properties and dynamics determined by soil. ENVO:01001048 envoEmpo envoOmics sediment environment An environmental system which has its properties and dynamics determined by sediment. ENVO:01001055 envoEmpo envoMeo envoOmics environment associated with an animal part or small animal An environmental system determined by part of a living or dead animal, or a whole small animal. ENVO:01001057 envoEmpo envoMeo envoOmics environment associated with a plant part or small plant An environmental system determined by part of a living or dead plant, or a whole small plant. ENVO:01001069 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 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 A material which is composed primarily of one or more pure metals and which shows their properties. ENVO:01001110 LTER:173 This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here. ecosystem An environmental system which includes both living and non-living components. LTER:173 http://129.24.124.196/vocab/vocab/index.php?tema=173&/ecosystems ENVO:01001125 This class is defined logically - any material that is frozen is considered a subclass. Note that ice may be formed at very high temperatures, due to gravitational effects and/or pressure. ice An ice is an environmental material which is either frozen or which is maintained in a solid state by gravitational forces or pressure. ENVO:01001176 http://purl.jp/bio/11/meo/MEO_0000871 envoMeo envoOmics environment associated with an aquatic invertebrate An environment which has its properties and composition largely determined by the presence of a metazoan which lacks a vetebral column and which has a habitat that is found in an aquatic environmental system. http://purl.jp/bio/11/meo/MEO_0000871 Not currently live, may need to be switched to alternative PURLs. ENVO:01001191 EcoLexicon:surface_water SWEETRealm:SurfaceWater https://en.wikipedia.org/wiki/Surface_water surface of a body of water water body surface water surface The surface layer of a volume of water. ENVO:01001192 surface of a sedimentary mass surface sediment sediment surface The surface layer of a mass of sediment. ENVO:01001199 terrestrial environmental zone An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it. ENVO:01001201 This class will eventually be populated by inference alone, with its subclasses distributed in more process-linked hierarchies to improve semantic density. marine environmental zone An environmental zone which is bounded by material parts of a marine environment. ENVO:01001209 EcoLexicon:wetland FTT:1001 FTT:1060 FTT:1061 FTT:1118 FTT:1180 FTT:1190 FTT:1206 FTT:1207 FTT:1226 FTT:184 FTT:185 FTT:228 FTT:281 FTT:480 FTT:716 FTT:883 FTT:934 FTT:945 FTT:983 Geonames:H.WTLD LTER:630 SPIRE:Bog SWEETRealm:Wetland TGN:21301 TGN:21304 TGN:21305 https://en.wikipedia.org/wiki/Wetland Wetland Estuarine Wetland Lacustrine Wetland Marine Wetland Palustrine Wetland Riparian Wetland Terrestial Wetland back marsh backswamp backwater barrier flat blanket bog bog cienaga dismal everglade floating marsh forested wetland marsh mire mud flat peat cutting area peatland quagmire quaking bog riparian area slash slough slue swamp forest tulelands moor morass muskeg wetland ecosystem A terrestrial ecosystem which is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances does support, a prevalence of vegetation typically adapted for life in saturated soil conditions. Wetland NASA:earthrealm Wetland USGS:SDTS Estuarine Wetland NASA:earthrealm Lacustrine Wetland NASA:earthrealm Marine Wetland NASA:earthrealm Palustrine Wetland NASA:earthrealm Riparian Wetland NASA:earthrealm Terrestial Wetland NASA:earthrealm back marsh USGS:SDTS backswamp USGS:SDTS backwater ADL:FTT barrier flat USGS:SDTS blanket bog USGS:SDTS bog ADL:FTT bog Getty:TGN cienaga ADL:FTT dismal USGS:SDTS everglade USGS:SDTS floating marsh USGS:SDTS forested wetland ADL:FTT marsh ADL:FTT mire ADL:FTT mire USGS:SDTS mud flat ADL:FTT peat cutting area ADL:FTT peatland ADL:FTT quagmire ADL:FTT quagmire USGS:SDTS quaking bog USGS:SDTS riparian area ADL:FTT slash USGS:SDTS slough ADL:FTT slough Getty:TGN slough USGS:SDTS slue ADL:FTT swamp forest USGS:SDTS tulelands USGS:SDTS moor USGS:SDTS morass USGS:SDTS muskeg USGS:SDTS ENVO:01001226 terrestrial natural environment A natural environment which is located on a land mass. ENVO:01001227 aquatic natural environment A natural environment which is within a water body. ENVO:01001273 liquid layer A layer which is primarily composed of some liquid material. ENVO:01001275 solid layer A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid. ENVO:01001276 water ice layer A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid. ENVO:01001299 atmospheric area atmospheric zone An environmental zone which is part of an atmosphere. ENVO:01001301 envoMarine envoPolar aquatic estuarine layer A layer of liquid that is part of an estuary. ENVO:01001305 ORCID:0000-0002-4366-3088 envoPolar vegetated area A vegetated area is a geographic feature which has ground cover dominated by plant communities. ENVO:01001309 liquid air-water interface layer A liquid surface layer which is in contact with air. ENVO:01001311 solid surface layer A surface layer which is composed primarily of solid environmental material. ENVO:01001334 advective transport Advective processes are disjoint from diffusive processes. Typically, fluids are advected. advective transport process A material transport process during which a volume of material is displaced due to a disequilibrium in physical forces and during which 1) the qualities that inhere in that volume and 2) the processes that are unfolding within it are largely unchanged. ENVO:01001346 erosion An action of exogenic processes (such as water flow or wind) which remove environmental material from one location on the surface of an astronomical body, transporting it to another location where it is deposited. ENVO:01001434 http://orcid.org/0000-0002-4366-3088 anthropogenic ecosystem conversion process A process during which an ecosystem - natural or anthropised - is changed by the actions of humans. ENVO:01001510 http://orcid.org/0000-0002-4366-3088 congelation congelation process Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question. material congelation process A material transformation process during which a material's viscosity increase either through a reduction in temperature or through chemical reactions. Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question. https://en.wikipedia.org/wiki/Congelation ENVO:01001526 http://orcid.org/0000-0002-4366-3088 frozen soil Soil which is below the freezing point of water. ENVO:01001554 http://orcid.org/0000-0002-4366-3088 surface layer of a water body A water surface that is part of a water body. ENVO:01001570 http://orcid.org/0000-0002-4366-3088 https://www.worldwildlife.org/biome-categories/terrestrial-ecoregions terrestrial ecoregion An ecoregion which is located on a landmass. ENVO:01001581 http://orcid.org/0000-0002-4366-3088 envoMarine At this level, the depth of this layer is ambiguous. Some methods (telemetry) measure only the first few centimeters of the sea or ocean surface. In situ methods often sample the first few meters. Subclasses can be created for such cases. sea surface layer A surface layer of a water body which is part of an ocean or sea. ENVO:01001785 land A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water. ENVO:01001795 ecosystem process An environmental process either driven by or primarily impacting the parts or emergent properties of an ecosystem. ENVO:02500000 This is a convenience class for organisation and should not be used for annotation. environmental system process A process in which includes the components of an environmental system as participants. ENVO:02500003 This class will be populated by inference and is primarily organisational. atmospheric process A process which occurs within an atmosphere. ENVO:02500027 anthropogenic environmental process An environmental process which is driven by the action of humans. ENVO:02500031 This classes asserted subclasses will be moved away as it should be an inferred class. hydrological process An environmental process which has water - in any of its states - as a participant. ENVO:03000009 http://orcid.org/0000-0002-3410-4655 http://orcid.org/0000-0002-4366-3088 envoPolar Experimental class for structural purposes not recommended for annotation. A material accumulation process ends a material transport process. material accumulation process A process during which the mass of one or more materials, present within a given site, increases. ENVO:03000010 http://orcid.org/0000-0002-3410-4655 http://orcid.org/0000-0002-4366-3088 envoPolar Experimental class for structural purposes not recommended for annotation. material transport process A process during which material is displaced from its original location and transported either to a new location or back to the original location. ENVO:03000033 http://orcid.org/0000-0002-3410-4655 http://orcid.org/0000-0002-4366-3088 marine sediments envoPolar 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 Sediment which has been transported through the marine water column, settling on the seafloor. ENVO:03000036 http://orcid.org/0000-0002-3410-4655 http://orcid.org/0000-0002-4366-3088 envoPolar sedimentation in a water body A material accumulation process during which solid particles are pulled through a water body by gravitation or centrifugal force and which ends when they settle on a solid surface. ENVO:03000043 A different material transformation process class (or similarly named class) pertaining to the conversion of a specific chemical into another belongs in CHEBI and or REX ontologies. http://orcid.org/0000-0002-3410-4655 http://orcid.org/0000-0002-4366-3088 envoPolar Experimental class for structural purposes not recommended for annotation. A material transformation process only refers to ENVO:environmental material classes (e.g. bulk and typically impure substances), rather than transformations converting a specific chemical into another. material transformation process A process during which a portion of some environmental material is converted into a different material or a collection of materials. ENVO:09200004 soil porosity porosity of soil The porosity of some soil. ENVO:09200008 soil composition composition of soil The composition of some soil. ENVO:09200009 soil structure structure of soil The structure of some soil. ENVO:09200013 soil wetness wetness of soil The wetness of some soil. ENVO:09200017 water composition composition of water The composition of some water. ENVO:2100000 anatomical entity environment true An environment which is determined by an anatomical entity. GEO:000000334 subcontinental land mass GEO:000000335 contiguous continental land mass per the definition of 'contiguous' of "being in actual contact : touching along a boundary or at a point", these land masses share boundaries with other land masses that are part of the same continent, and thus are not surrounded by water like an island. At some point, we need an 'adjacent to' relation if BFO doesn't provide it. One question is whether this class encompasses fiat parts of islands. contiguous land mass GEO:000000357 William R. Hogan It cannot be a part of the island, for example, that is below water. contiguous island land mass A subcontinental land mass that is part of an island and includes part of the land surface of the island. GEO:000000369 aggregate of contiguous land masses GEO:000000372 François Modave Mathias Brochhausen Matt Diller William R. Hogan geographical location geographical region A geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface. GEO:000000375 land mass GEO:000000390 aggregate of islands GEO:000000787 geodetic coordinate measurement datum A measurement of location on the Earth that uses a single number to specify a coordinate in a coordinate system known as a geodetic datum. Josh Hanna William R. Hogan latitude and longitude are key subtypes geodetic coordinate measurement datum GEO:000000788 geodetic datum A coordinate system, and a set of reference points, used to locate places on the Earth (or similar objects). Wikipedia: https://en.wikipedia.org/wiki/Geodetic_datum Date accessed: 2015-04-13 Josh Hanna William R. Hogan Every latitude and longitude measurement is with respect to a geodetic datum. Most common ones in use are NAD83 and WGS84. geodetic datum GEO:000000789 planar angular measurement unit label plane angle measurement unit label GO:0019952 GO:0050876 Wikipedia:Reproduction reproductive physiological process biological_process GO:0000003 reproduction The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GO:0000003 GO:0008150 biological process physiological process single organism process single-organism process biological process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. GO:0048590 biological_process growth pattern non-developmental growth GO:0040007 See also the biological process term 'cell growth ; GO:0016049'. growth The increase in size or mass of an entire organism, a part of an organism or a cell. GO:0040007 non-developmental growth GOC:mah IAO:0000003 measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A data item label that denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. http://purl.obolibrary.org/obo/obi.owl PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label IAO:0000009 data item label An information content entity that is part of some data item and is used to partially define the denotation of that data item. http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n datum label 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. http://purl.obolibrary.org/obo/obi.owl GROUP: IAO data item label IAO:0000027 a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. data item IAO:0000030 A generically dependent continuant that is about some thing. information content entity IAO:0000032 scalar measurement datum 10 feet. 3 ml. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. http://purl.obolibrary.org/obo/obi.owl PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum IAO:0000078 curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 PERSON:Bill Bug curation status specification IAO:0000102 data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part IAO:0000109 measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? OBI_0000305 group:OBI http://purl.obolibrary.org/obo/obi.owl person:Chris Stoeckert measurement datum IAO:0000225 obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification IAO:0000409 The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Barry Smith, Werner Ceusters Alan Ruttenberg denotator type IAO:8000000 I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. ontology file This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. cjm 2018-05-20T20:55:03Z ontology module IAO:8000001 An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. cjm 2018-05-20T20:55:30Z base ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000002 An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. source ontology module cjm 2018-05-20T20:55:47Z editors ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000003 An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module cjm 2018-05-20T20:56:13Z main release ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000004 An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. cjm 2018-05-20T20:56:23Z bridge ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000005 A subset ontology module that is intended to be imported from another ontology. TODO: add axioms that indicate this is the output of a module extraction process. import file cjm 2018-05-20T20:56:47Z import ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000006 An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. ontology slim subset ontology cjm 2018-05-20T20:58:11Z subset ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000007 A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. cjm 2018-05-20T20:58:38Z curation subset ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000008 An ontology module that is intended for usage in analysis or discovery applications. cjm 2018-05-20T20:58:49Z analysis subset ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000009 A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. ribbon subset cjm 2018-05-20T20:59:19Z single layer subset ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000010 A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. antislim cjm 2018-05-20T20:59:57Z exclusion subset ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000011 An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import cjm 2018-05-20T21:00:14Z external import ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000012 A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset cjm 2018-05-20T21:14:16Z species subset ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000013 An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. cjm 2018-05-20T21:20:33Z reasoned ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000014 An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process cjm 2018-05-20T21:21:12Z generated ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000015 An ontology module that is automatically generated from a template specification and fillers for slots in that template. cjm 2018-05-20T21:21:21Z template generated ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000016 cjm 2018-05-20T21:28:15Z taxonomic bridge ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000017 cjm 2018-05-22T04:15:54Z ontology module subsetted by expressivity <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000018 A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports cjm 2018-05-22T04:16:10Z obo basic subset ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000019 cjm 2018-05-22T04:16:28Z ontology module subsetted by owl profile <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true IAO:8000020 cjm 2018-05-22T04:16:48Z el++ ontology module <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true NCBITaxon:10239 Vira Viridae viruses Vira Viridae NCBITaxon:117565 GC_ID:1 fish fishes ncbi_taxonomy Agnatha Hyperotreti myxini fish fishes Agnatha Hyperotreti NCBITaxon:117569 GC_ID:1 Petromyzontida fish fishes ncbi_taxonomy Agnatha Cephalaspidomorphi Monorhina hyperoartia fish fishes Agnatha Cephalaspidomorphi Monorhina NCBITaxon:117570 teleostomi NCBITaxon:117571 bony vertebrates euteleostomi bony vertebrates NCBITaxon:1206794 GC_ID:1 ncbi_taxonomy ecdysozoa NCBITaxon:1206795 GC_ID:1 ncbi_taxonomy lophotrochozoa NCBITaxon:1294634 GC_ID:1 alligators and others ncbi_taxonomy Crocodilia Reptilia reptiles crocodylia alligators and others Crocodilia Reptilia reptiles NCBITaxon:131221 GC_ID:1 charophyte/embryophyte group ncbi_taxonomy Charophyta/Embryophyta group streptophytina charophyte/embryophyte group Charophyta/Embryophyta group NCBITaxon:1329799 GC_ID:1 PMID:22839753 PMID:25450099 ncbi_taxonomy Archosauria-Testudines Testudines + Archosauria group archelosauria Archosauria-Testudines Testudines + Archosauria group NCBITaxon:1338369 dipnotetrapodomorpha NCBITaxon:136419 GC_ID:1 ncbi_taxonomy cercozoans cercozoa cercozoans NCBITaxon:1437010 Boreotheria boreoeutheria Boreotheria NCBITaxon:1476529 GC_ID:1 jawless vertebrates ncbi_taxonomy Agnatha cyclostomata jawless vertebrates Agnatha NCBITaxon:197562 GC_ID:1 PMID:10874751 PMID:11557979 ncbi_taxonomy pancrustacea NCBITaxon:197563 GC_ID:1 PMID:11557979 PMID:9727836 mandibulates ncbi_taxonomy mandibulata mandibulates NCBITaxon:2 eubacteria Monera Procaryotae Prokaryota Prokaryotae bacteria not Bacteria Haeckel 1894 prokaryote prokaryotes bacteria eubacteria Monera Procaryotae Prokaryota Prokaryotae bacteria not Bacteria Haeckel 1894 prokaryote prokaryotes NCBITaxon:207598 Homo/Pan/Gorilla group homininae Homo/Pan/Gorilla group NCBITaxon:2157 Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes archaea Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes NCBITaxon:2608109 GC_ID:1 PMID:30257078 ncbi_taxonomy haptista NCBITaxon:2611352 GC_ID:1 ncbi_taxonomy discoba NCBITaxon:2697495 GC_ID:1 ncbi_taxonomy spiralia NCBITaxon:2698737 GC_ID:1 ncbi_taxonomy SAR supergroup sar SAR supergroup GC_ID:1 PMID:23020233 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes NCBITaxon:2759 eukaryota NCBITaxon:2759 eucaryotes eucaryotes eukaryotes eukaryotes Eucarya Eucarya Eucaryotae Eucaryotae Eukarya Eukarya Eukaryotae Eukaryotae eukaryotes eukaryotes NCBITaxon:2763 GC_ID:1 red algae rhodophytes ncbi_taxonomy Rhodophyceae Rhodophycota algae red algae rhodophyta red algae rhodophytes Rhodophyceae Rhodophycota algae red algae NCBITaxon:2830 GC_ID:1 coccolithophorids ncbi_taxonomy Chromophyta Haptophyceae Prymnesiophyta algae haptophytes haptophyta coccolithophorids Chromophyta Haptophyceae Prymnesiophyta algae haptophytes NCBITaxon:2841271 GC_ID:1 ncbi_taxonomy testudinata NCBITaxon:2864 GC_ID:1 Dinoflagellata dinoflagellates dinophytes ncbi_taxonomy Chromophyta Dinoflagellata Dinophycidae Dinophyta Pyrrhophyta Pyrrophyta algae dinoflagellates dinophyceae dinoflagellates dinophytes Chromophyta Dinoflagellata Dinophycidae Dinophyta Pyrrhophyta Pyrrophyta algae dinoflagellates NCBITaxon:29197 GC_ID:1 PMID:7874738 chlorarachniophytes ncbi_taxonomy Chlorarachnida Chlorarachniophyta algae chlorarachniophyceae chlorarachniophytes Chlorarachnida Chlorarachniophyta algae NCBITaxon:3027 NCBITaxon:2895 GC_ID:1 Cryptophyta cryptomonads ncbi_taxonomy Chromophyta Cryptomonadida algae cryptomonads cryptophytes cryptophyceae cryptomonads Chromophyta Cryptomonadida algae cryptomonads cryptophytes NCBITaxon:3035 NCBITaxon:2570883 GC_ID:1 PMID:12812373 euglenids euglenophytes ncbi_taxonomy Euglenoida Euglenophyta algae euglenoids euglenida euglenids euglenophytes Euglenoida Euglenophyta algae euglenoids NCBITaxon:3041 GC_ID:1 PMID:23020233 green algae ncbi_taxonomy Chlorophycota Chlorophyta sensu Bremer 1985 algae green algae chlorophyta green algae Chlorophycota Chlorophyta sensu Bremer 1985 algae green algae NCBITaxon:314146 euarchontoglires NCBITaxon:314293 Anthropoidea simiiformes Anthropoidea NCBITaxon:314295 ape apes hominoidea ape apes NCBITaxon:3193 GC_ID:1 higher plants land plants plants ncbi_taxonomy embryophyta higher plants land plants plants NCBITaxon:32523 tetrapods tetrapoda tetrapods NCBITaxon:32524 amniotes amniota amniotes NCBITaxon:32525 Theria theria <mammalia> Theria NCBITaxon:32561 GC_ID:1 diapsids ncbi_taxonomy Diapsida sauria diapsids Diapsida NCBITaxon:33090 GC_ID:1 PMID:16248873 PMID:30257078 Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants ncbi_taxonomy Chlorobionta Chloroplastida green plants viridiplantae Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants Chlorobionta Chloroplastida green plants GC_ID:1 ncbi_taxonomy Fungi/Metazoa group opisthokonts NCBITaxon:33154 opisthokonta NCBITaxon:33154 Fungi/Metazoa group Fungi/Metazoa group opisthokonts opisthokonts NCBITaxon:33213 bilateria NCBITaxon:33317 GC_ID:1 ncbi_taxonomy protostomia NCBITaxon:33511 deuterostomes deuterostomia deuterostomes NCBITaxon:33630 GC_ID:1 alveolates ncbi_taxonomy alveolata alveolates NCBITaxon:33634 GC_ID:1 heterokonts ncbi_taxonomy Chromophyta Heterokonta Straminipila stramenopiles heterokonts Chromophyta Heterokonta Straminipila NCBITaxon:33682 GC_ID:1 ncbi_taxonomy Euglenozoans euglenozoa Euglenozoans NCBITaxon:35493 GC_ID:1 ncbi_taxonomy streptophyta NCBITaxon:376913 haplorrhini NCBITaxon:38254 GC_ID:1 Glaucophyta glaucocystophytes ncbi_taxonomy Glaucophyceae algae glaucocystophyceae glaucocystophytes Glaucophyceae algae NCBITaxon:40674 mammals mammalia mammals NCBITaxon:436486 GC_ID:1 dinosaur dinosaurs ncbi_taxonomy dinosauria dinosaur dinosaurs NCBITaxon:436489 GC_ID:1 ncbi_taxonomy saurischia NCBITaxon:436491 GC_ID:1 ncbi_taxonomy theropoda NCBITaxon:436492 GC_ID:1 ncbi_taxonomy coelurosauria NCBITaxon:4751 GC_ID:1 PMID:11062127 PMID:12684019 ncbi_taxonomy Mycota fungi Mycota NCBITaxon:4762 GC_ID:1 ncbi_taxonomy Peronosporomycetes oomycetes oomycota Peronosporomycetes oomycetes oomycetes NCBITaxon:50557 GC_ID:1 true insects ncbi_taxonomy insects insecta true insects insects NCBITaxon:543769 GC_ID:1 PMID:30257078 ncbi_taxonomy rhizaria NCBITaxon:58023 GC_ID:1 vascular plants ncbi_taxonomy tracheophyta vascular plants NCBITaxon:6447 GC_ID:1 molluscs mollusks ncbi_taxonomy mollusca molluscs mollusks NCBITaxon:6656 GC_ID:1 arthropods ncbi_taxonomy arthropods arthropoda arthropods arthropods NCBITaxon:6657 GC_ID:1 crustaceans ncbi_taxonomy crustacea crustaceans NCBITaxon:6960 GC_ID:1 insects ncbi_taxonomy Atelocerata Tracheata Uniramia hexapods hexapoda insects Atelocerata Tracheata Uniramia hexapods NCBITaxon:7711 chordates chordata chordates NCBITaxon:7742 Vertebrata vertebrates vertebrata <metazoa> Vertebrata vertebrates NCBITaxon:7776 Gnathostomata jawed vertebrates gnathostomata <vertebrate> Gnathostomata jawed vertebrates NCBITaxon:7777 GC_ID:1 cartilaginous fishes fish fishes ncbi_taxonomy cartilaginous fishes chondrichthyes cartilaginous fishes fish fishes cartilaginous fishes NCBITaxon:7878 GC_ID:1 dipnoans fish fishes lungfishes ncbi_taxonomy Choanichthyes Dipneusti Dipnoi Osteichthyes lungfishes dipnomorpha dipnoans fish fishes lungfishes Choanichthyes Dipneusti Dipnoi Osteichthyes lungfishes NCBITaxon:7898 GC_ID:1 fish fishes ray-finned fishes ncbi_taxonomy Actinopterygi Osteichthyes bony fishes actinopterygii fish fishes ray-finned fishes Actinopterygi Osteichthyes bony fishes NCBITaxon:8287 sarcopterygii NCBITaxon:8292 GC_ID:1 amphibians ncbi_taxonomy amphibia amphibians NCBITaxon:8457 GC_ID:1 sauropsids ncbi_taxonomy sauropsida sauropsids NCBITaxon:8459 GC_ID:1 PMID:22839753 PMID:25450099 anapsid reptiles turtles ncbi_taxonomy Anapsida Reptilia reptiles testudines anapsid reptiles turtles Anapsida Reptilia reptiles NCBITaxon:8492 GC_ID:1 ncbi_taxonomy archosauria NCBITaxon:8504 GC_ID:1 PMID:22982760 lepidosaurs ncbi_taxonomy Reptilia lizards reptiles lepidosauria lepidosaurs Reptilia lizards reptiles NCBITaxon:8782 GC_ID:1 birds ncbi_taxonomy avian aves birds avian NCBITaxon:88770 GC_ID:1 ncbi_taxonomy panarthropoda NCBITaxon:89593 Craniata craniata <chordata> Craniata NCBITaxon:9347 eutherian mammals placental mammals placentals Placentalia eutheria eutherian mammals placental mammals placentals Placentalia NCBITaxon:9443 primate Primata primates primate Primata NCBITaxon:9526 catarrhini NCBITaxon:9604 great apes Pongidae hominidae great apes Pongidae NCBITaxon:9605 humans homo humans NCBITaxon:9606 human man humans homo sapiens human man NCIT:C122929 C122929 Phenomenon or Process C4049986 Impacted impact The effect or consequence of an event or condition. NCIT:C127787 C127787 Quantitative Concept CDISC TOTNUM total number A measurement of the total number of entities. The determination of the amount of total number of entities. NCIT:C153298 C153298 Conceptual Entity C0023980 lifespan longevity The length or duration of life or viability. NCIT:C16632 Any demarcated area of the Earth; may be determined by both natural and human boundaries. C16632 Geographic Area Geographic Area C0017446 CDISC Any demarcated area of the Earth; may be determined by both natural and human boundaries, such as a state or province. Geographic_Area Area Geographic Area Geographic Location Geographic Region Region Geographic Area NCIT:C16977 C16977 Organism Attribute C0031437 phenotype The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment. The observable characteristics in an individual resulting from the expression of genes; the clinical presentation of an individual with a particular genotype. NCIT:C171083 C171083 Qualitative Concept individual trait organism characteristic A characteristic or attribute inherent or inherited to an organism. NCIT:C171088 C171088 Conceptual Entity population group attribute population group feature population group property population group trait population group characteristic A characteristic or attribute of a population group. NCIT:C178428 C178428 Geographic Area urban urbanized area A delineated geographic area encompassing residential, commercial, and other non-residential urban land uses with a residential population of 50,000 or more people and a density of 1,000 people or more per square mile. NCIT:C178430 C178430 Geographic Area C0178837 rural rural area A non-urbanized geographic area. "Rural" encompasses densely settled small towns with a residential population of less than 2,500 people, more sparsely populated areas, and remote areas. NCIT:C20181 An organizational header for concepts representing mostly abstract entities. C20181 Classification Conceptual Entity C1254372 Conceptual_Entities Conceptual Entity conceptual entity NCIT:C25256 C25256 Quantitative Concept C1265611 BRIDG amount quantity How much there is of something that you can measure; the total amount or number. NCIT:C25319 C25319 Spatial Concept C0442504 BRIDG place A bounded physical location which may contain structures. EXAMPLE(S): ambulance, helicopter, manufacturing site, service delivery location, home, emergency department, surgical suite, patient room. NOTE(S): Constraints: Place may be natural or man-made. The geographic position of a place may or may not be constant. Discussion: Places may be work facilities (where relevant acts occur), homes (where people live) or offices (where people work). Places may contain sub-places (floor, room, booth, bed). Places may also be sites that are investigated in the context of health care, social work, public health administration (e.g., buildings, picnic grounds, day care centers, prisons, counties, states, and other focuses of epidemiological events). The particular portion of space occupied by a physical object or intended for a physical object. NCIT:C25334 C25334 Conceptual Entity C1444754 CDISC FDA NICHD length The linear extent in space from one end of something to the other end, or the extent of something from beginning to end. NCIT:C25345 C25345 Quantitative Concept C0487742 CDISC FDA wideness width The extent or measurement of something from side to side. NCIT:C25347 C25347 Quantitative Concept C0489786 CDISC FDA NCPDP height The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension. Vertical measurement value. NCIT:C25387 C25387 Idea or Concept C0814225 benefit The positive effects of something. NCIT:C25446 The act of alteration or modification; changed or altered in form or character. C25446 Qualitative Concept Change C0392747 Change Adapt Adapted Change Changed Modification Modified change NCIT:C25472 C25472 Temporal Concept C0439596 DIPG/DMG ICDC UCUM cycles cyclic cylical cycle An event or sequence of events that constitute a round or succession of observable phenomena, recurring usually at regular or approximately regular time intervals and in the same sequence. NCIT:C25499 C25499 C0441471 event Something that happens at a given place and time. NCIT:C25548 To have a connection by participation or association or use; sharing in an activity or process. C25548 Qualitative Concept Involvement C1314939 Involvement Involved Involvement involvement NCIT:C25688 C25688 Qualitative Concept C0449438 CTRP status A condition or state at a particular time. NCIT:C37927 C37927 Qualitative Concept C0009393 CDISC Colour color The appearance of objects (or light sources) described in terms of a person's perception of their hue and lightness (or brightness) and saturation. NCIT:C40098 C40098 Conceptual Entity C1515221 biological taxon taxonomy taxon Ranked categories for the classification of organisms according to their suspected evolutionary relationships. NCIT:C41129 C41129 Spatial Concept C0205147 region An area or portion of something with more or less definite boundaries designed or specified according to some established biological, administrative, economic, demographic, etc. criteria. NCIT:C42703 C42703 Conceptual Entity C0439659 origin The place where something begins or comes from in either the sense of a physical location or a metaphysical source. NCIT:C43428 C43428 Spatial Concept C1710706 zonal zone An area or region distinguished from adjacent parts by a distinctive feature or characteristic. Specifies the location of a zone on an array. (caMAGE) NCIT:C45293 C45293 Conceptual Entity C1705920 species A group of organisms that differ from all other groups of organisms and that are capable of breeding and producing fertile offspring. NCIT:C45997 Quantity of dimension one used to express on a scale from 0 to 14 the amount-of-substance concentration of hydrogen ion of dilute aqueous solution, calculated as the logarithm of the reciprocal of hydrogen-ion concentration in gram atoms per liter. C45997 Phenomenon or Process pH pH C4048290 CDISC CTRP FDA UCUM The negative logarithm (base 10) of the concentration of hydronium ions, which is used as a measure of the acidity or alkalinity of a fluid. pH PH [pH] pH potential of Hydrogen pH NCIT:C47882 C47882 Quantitative Concept C1705117 incremental step increment The amount by which something increases. NCIT:C48058 The capacity of a physical system to do work. C48058 Natural Phenomenon or Process Energy C0542479 Energy Energy energy NCIT:C48952 C48952 Geographic Area C0022130 isle island A land mass smaller than a continent that is surrounded by water. NCIT:C48956 C48956 Geographic Area C3714523 geographic section section A distinct region or subdivision of a territorial or political area or community. NCIT:C61556 C61556 Conceptual Entity C1880266 defense A trait or behaviour that is useful for repelling an enemy. Protection from harm. NCIT:C64203 C64203 Spatial Concept C0027569 neighborhood A surrounding or nearby region. NCIT:C71612 C71612 Spatial Concept C1295726 perimeter The size of something as given by the distance around it. NCIT:C88206 C88206 Conceptual Entity C0020167 humidity A measure of the water vapor content of air. NCIT:C89276 C89276 Qualitative Concept C0518031 endurance The ability to sustain an activity over a period of time. NCIT:C90395 C90395 Quantitative Concept C2983614 CDISC humidt housing humidity The amount of water vapor in the air of a living space. The percentage of ambient moisture of a living space. OBI:0001620 latitude coordinate measurement datum A measurement datum that is the measure of the latitude coordinate of a site. latitude NIAID GSCID-BRC metadata working group http://purl.obolibrary.org/obo/obi.owl Specimen Collection Location - Latitude NIAID GSCID-BRC Person: Chris Stoeckert, Jie Zheng latitude coordinate measurement datum <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true OBI:0001621 longitude coordinate measurement datum A measurement datum that is the measure of the longitude coordinate of a site. longitude NIAID GSCID-BRC metadata working group http://purl.obolibrary.org/obo/obi.owl Specimen Collection Location - Longitude NIAID GSCID-BRC Person: Chris Stoeckert, Jie Zheng longitude coordinate measurement datum <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true OBI:0001931 scalar value specification A value specification that consists of two parts: a numeral and a unit label http://purl.obolibrary.org/obo/obi.owl PERSON:Bjoern Peters scalar value specification <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true OBI:0001933 value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. http://purl.obolibrary.org/obo/obi.owl PERSON:Bjoern Peters value specification <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true PATO:0000001 trait quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATO:0000025 composed of compositionality content structure, composition composition A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. PATO:0000051 morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. PATO:0000052 relational shape quality shape A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATO:0000117 size A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. PATO:0000125 weight mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. PATO:0000140 location placement relational spatial quality position A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATO:0000141 conformation relational structural quality structure A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATO:0000957 opacity An optical quality which obtains by virtue of the ability of the bearer to absorb visible light. PATO:0000963 non-transparent clouding cloudy opaque A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy. PATO:0000970 permeability A structural quality inhering in a bearer by virtue of the bearer's disposition to being permeated or pervaded by a gas or liquid (as by osmosis or diffusion). PATO:0000973 porosity A permeability quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices. PATO:0000984 porous A porosity quality inhering in a bearer by virtue of the bearer's being capable of admitting the passage of gas or liquid through pores or interstices. PATO:0001018 relational physical quality physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0001154 elongated A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width. PATO:0001230 strength A quality inhering in a bearer by virtue of the bearer's power or force. PATO:0001241 monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant physical object quality A quality which inheres in a continuant. PATO:0001291 electromagnetic (em) radiation quality A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. PATO:0001300 optical quality An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. PATO:0001332 amorphous A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology. PATO:0001481 sloped A shape quality inhering in a bearer by virtue of the bearer's having an oblique or slanted direction. PATO:0001687 elevation A positional quality inhering in a bearer by virtue of the bearer's vertical distance of a point above or below a reference surface. PATO:0001739 radiation quality A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. PATO:0001759 granular A composition quality inhering in a bearer by virtue of the bearer's containing granules. PATO:0001822 wetness A quality inhering in a bearer by virtue of whether the bearer's being covered by a liquid. PATO:0001823 wet A wetness quality inhering in a bearer by virtue of the bearer's being covered by a liquid. PATO:0002124 laminar A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. PATO:0002143 sloped downward PATO:0002181 displaced A positional quality inhering in a bearer by virtue the bearer's being changed in position. PATO:0002198 quality of a substance A quality inhering in a bearer by virtue of its constitution. 2 PCO:0000000 collection of organisms collection of organisms A material entity that consists of two or more organisms, viruses, or viroids. 1 PCO:0000001 population of organisms A collection of organisms, all of the same species, that live in the same place. 1 PCO:0000018 single-species collection of organisms A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. 2 PCO:0000029 multi-species collection of organisms A collection of organisms that consists of two or more organisms from at least two species. UBERON:0000061 biological structure connected biological structure anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. UBERON:0034768 morphological attribute morphological characteristic morphological property morphological trait morphological feature A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology. A unit which is a standard measure of the amount of a 2-dimensional flat surface. http://purl.obolibrary.org/obo/uo.owl george gkoutos unit.ontology UO:0000047 area unit UO:0000047 <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true oboInOwl:DbXref <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true oboInOwl:Definition <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true oboInOwl:Subset <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true oboInOwl:Synonym <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true oboInOwl:SynonymType <_000131 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true owl:Thing INBIO:_000000 See http://purl.obolibrary.org/obo/RO_0002577 system A material entity consisting of multiple components that are causally integrated. INBIO:_000001 disturbance A disturbance is an event or process that disrupts ecosystem, community or population structure, and changes resources, substrate availability or the physical environment. Disturbances can have anthropogenic or non-anthropogenic causes. INBIO:_000002 See http://purl.bioontology.org/ontology/MESH/D018977 micronutrient Essential dietary elements or organic compounds that are required in only small quantities for normal physiologic processes to occur. INBIO:_000003 establishment INBIO:_000004 From http://www.fao.org/aims/aos/cwr.owl#PopulationSize population size taille d'une population tamaño de la población размер популяции It's the amount of individuals in a population INBIO:_000005 Alien species that become established and spread beyond the place of introduction are called invasive species. invasive species Alien species that sustain self-replacing populations over several life cycles, produce reproductive offspring, often in very large numbers at considerable distance from the parent and/or site of introduction, and have the potential to spread over long distances. INBIO:_000006 See http://purl.bioontology.org/ontology/CSP/1035-7240 host organism interaction interactions between one organism and another which it harbors or nourishes. INBIO:_000007 genetic attribute genetic feature genetic property genetic trait genetic characteristic Information about the genetic characteristics INBIO:_000008 from https://www.thefreedictionary.com/predator predator An organism that lives by preying on other organisms. INBIO:_000009 Adapted from https://en.wikipedia.org/wiki/Mineral_%28nutrient%29 mineral nutrient Chemical element required by organisms to perform functions necessary for life. INBIO:_000010 species diversity INBIO:_000011 introduction effort propagule pressure A composite measure consisting of the number of individuals introduced per introduction event and the frequency of introduction events. INBIO:_000012 See http://purl.bioontology.org/ontology/MESH/D000078622 nutrient Various components of food that are required for nourishment. INBIO:_000013 genetic change Any change in the genome of a species INBIO:_000014 successful INBIO:_000015 nutrient salt Nutrient occurring in the chemical form of salt INBIO:_000016 See http://purl.bioontology.org/ontology/MESH/D008027 light That portion of the electromagnetic spectrum in the visible, ultraviolet, and infrared range. INBIO:_000017 generation length INBIO:_000018 from https://www.thefreedictionary.com/parasite parasite An organism that lives and feeds on or in an organism of a different species and causes harm to its host. INBIO:_000019 ecosystem attribute ecosystem characteristic ecosystem feature ecosystem trait from http://www.openness-project.eu/taxonomy/term/73 ecosystem property Attributes which characterize an ecosystem, such as its size, biodiversity, stability, degree of organization, as well as its functions and processes (i.e. the internal exchanges of materials, energy and information among different pools). INBIO:_000020 environmental change change in environment Any change in the environment, e.g. concerning temperature, soil nutrients or biodiversity INBIO:_000021 resistance staying essentially unchanged despite the presence of disturbances INBIO:_000022 generalist generalist enemy A species that can survive and reproduce in a wide range of environmental conditions using a wide variety of resouces to do so. INBIO:_000023 Functional Role Generic Role Role, Generic See http://purl.obolibrary.org/obo/NCIT_C48835 role The usual or expected function of something; the part something plays in an action or event. INBIO:_000024 invasion spread phase phase of spreading in the alien range as part of the invasion process INBIO:_000025 See NCIt:C29862 See SNOMEDCT:415178003 See http://www.ifomis.org/bfo/1.1/span#ProcessualEntity process A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs. An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. INBIO:_000026 area A geographical region that can include land as well as water. INBIO:_000027 invasion phase Sequential phases during the invasion process. Typically, four different phases are distinguished: transport, introduction, establishment and spread. INBIO:_000028 secondary nutrient chemical elements required by organisms in moderate amounts; for plants, these are e.g. sulfur, calcium and magnesium INBIO:_000029 beta diversity index metric for estimating beta diversity INBIO:_000030 the effective number of different species that are represented in a collection of individuals, it consists of two components: species richness and species evenness. From http://cerrado.linkeddata.es/ecology/ccon#SpeciesDiversity species diversity index INBIO:_000031 presence Being or existing in a specified place or at the specified time. INBIO:_000032 invasion transport phase phase of transportation to the alien range as part of the invasion process INBIO:_000033 See http://purl.bioontology.org/ontology/CSP/1035-7338 symbiosis state of close, permanent, or obligatory contact between 2 species, usually of a mutually beneficial nature. INBIO:_000034 from https://encyclopedia2.thefreedictionary.com/geographic+entity geographical entity An entity or geographic feature that occupies a position in space about which data describing the attributes of the entity and its geographic location are recorded. INBIO:_000035 phenological change Any change in the phenology of a species INBIO:_000036 natural disturbance disturbance that happened by some event not directly caused by human activity, e.g. storms or land slides INBIO:_000037 alien range adventive range exotic range foreign range invaded range non-indigenous range non-native range nonindigenous range nonnative range An area in which a species occurs even though it lies outside its native range. INBIO:_000038 functional attribute functional characteristic functional feature functional property after Reiss, J., Bridle, J.R., Montoya, J.M. and Woodward, G. 2009. Emerging horizons in biodiversity and ecosystem functioning research. Trends Ecol. Evol., 24: 505-514, and McGill BJ, Enquist BJ, Weiher E, Westoby M (2006) Rebuilding community ecology from functional traits Trends Ecol Evol 21:178-185 functional trait A trait that strongly influences organismal performance, and that determines its effect on processes and its response to environmental factors INBIO:_000039 species evenness index INBIO:_000040 human involvement human activity Actions of human beings that have an influence on the environment and that are characteristic for human societies, i.e. they are linked to social, economic or other cultural processes. INBIO:_000041 Alien species which are not in the subgroup of invasive species are part of the subgroup non-invasive species. non-invasive species Alien species that is not an invasive species. INBIO:_000042 measure measurement estimate INBIO:_000043 http://soilslab.cfr.washington.edu From http://www.fao.org/aims/aos/cwr.owl#Diversity diversity 1) The variety of plant and animal taxa, including genes, amino acids, flowers, species, or populations. 2) The variety of plant and animal communities, forest types, stand conditions, age classes, and landscape components. INBIO:_000044 ecological estimate ecological measurement ecological measure metric for qualifying ecologically relevant characteristics, e.g. biodiversity or body length INBIO:_000045 geographic range geographical range range An area where a species is found in the wild. 2 1 INBIO:_000046 ecological community definition from: http://purl.obolibrary.org/obo/PCO_000000 community A community of at least two different species, living in a particular area. Must have at least two populations of different species as members. INBIO:_000047 change in individual Any change in an individual organism, e.g. concerning its size or life cycle stage INBIO:_000048 Reptiles reptilia INBIO:_000049 morphological change Any change in the morpholoy of a species INBIO:_000050 species attribute species characteristic species feature species property from https://doi.org/10.1016/j.tree.2006.02.002 species trait A well-defined, measurable property of organisms, usually measured at the individual level and used comparatively across species. INBIO:_000051 indigenous species native species indigenous species Species that have evolved in a given area or that arrived there by natural means, without the intentional or accidental intervention of humans from an area where they are native. INBIO:_000052 animal diversity Variety of animal species present in a location INBIO:_000053 adventive species alien species exotic species foreign species introduced species non-indigenous species non-native species nonindigenous species alien species Species whose presence in a region is attributable to human actions that enable them to overcome biogeographical barriers. INBIO:_000054 See http://purl.obolibrary.org/obo/OBI_0100026 organism A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. INBIO:_000055 specialist specialist enemy A species that can survive and reproduce only within a narrow range of environmental conditions using specific resources (e.g., a specific diet). INBIO:_000056 Protozoans protozoa INBIO:_000057 algae INBIO:_000058 native range indigenous range A range in which a species has evolved or in which it has arrived by natural means. INBIO:_000059 attribute characteristic feature property from http://purl.obolibrary.org/obo/NCIT_C25447 trait The distinguishing qualities or prominent aspect of a person, object, action, process, or substance. INBIO:_000060 from http://vivoweb.org/ontology/core#Continent continent A large contiguous landmass that is at least partially surrounded by water, together with any islands on its continental shelf. INBIO:_000061 plant nutrient chemical element required by plants to perform functions necessary for life INBIO:_000062 morphological phenotype The form and structure of an organism and its parts, including cells, that result from the interaction of its genotype and the environment. From Bio-Assay Ontology. INBIO:_000063 animal nutrient chemical element required by animals to perform functions necessary for life INBIO:_000064 biological invasion species invasion invasion The process of transportation, establishment and spread of organisms outside of their native range. INBIO:_000065 nutrient content Amount of nutrients contained in something, e.g in a defined volume of soil or water INBIO:_000066 from https://en.wikipedia.org/wiki/Beta_diversity beta diversity In ecology, beta diversity (β-diversity or true beta diversity) is the ratio between regional and local species diversity. INBIO:_000067 after https://www.thefreedictionary.com/allocation allocation To set apart or re-distribute for a special purpose INBIO:_000068 invasion success Completing one or all phases of the invasion process. INBIO:_000069 invasion establishment phase phase of establishment in the alien range as part of the invasion process INBIO:_000070 from http://www.projecthalo.com/aura#Ectoparasite ectoparasite A parasite that lives on and feeds from the external surface of the host's body. INBIO:_000071 Fish Fishes pisces INBIO:_000072 primary nutrient chemical elements required by organisms in large amounts; for plants, these are nitrogen, phosphorus, and potassium INBIO:_000073 behavioural change Any change in the behaviour of a species INBIO:_000074 life history characteristic life history feature life history property life histrory attribute life history trait INBIO:_000075 not present absence Not existing in a specified place at a specified time. INBIO:_000076 population survival The process of remaining alive or in existence. INBIO:_000077 natality natality rate The rate in which new borns are added to a population, or in other words, the number of new borns over time. birth rate INBIO:_000078 in progress INBIO:_000079 resource Abiotic environmental factor necessary for survival, growth, and reproduction, such as water, light, mineral nutrients, and various forms of fixed carbon (e.g. plant material or meat). INBIO:_000080 plant diversity Variety of plant species present in a location INBIO:_000081 undisturbed ecosystem An ecosystem that has not been subject to disturbance. INBIO:_000082 Blackwell’s concise encyclopedia of ecology, 1999 From http://www.fao.org/aims/aos/cwr.owl#PopulationDensity densidad de población densité de population population density густота популяции The number of individuals per unit area. INBIO:_000083 compound attribute compound characteristic compound feature compound trait compound property Attribute resulting from a combination of several traits INBIO:_000084 from https://www.thefreedictionary.com/subcontinent subcontinent A large landmass, such as India, that is part of a continent but is considered either geographically or politically as an independent entity. INBIO:_000085 physiological change Any change in the physioloy of a species INBIO:_000086 See http://purl.bioontology.org/ontology/MESH/D014131 trace element A group of chemical elements that are needed in minute quantities for the proper growth, development, and physiology of an organism. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) INBIO:_000087 species richness index INBIO:_000088 environmental impact impact ecological impact A measurable change to the properties of an ecosystem by a non-native species. INBIO:_000089 competitive strength A species is strongly competitive, if its way of using shared resources usually leads to a reduction in survivorship, growth and/or reproduction of at least some of the competing individuals of the other species. INBIO:_000090 phenotypic plasticity The capacity of a genotype to produce different phenotypes in different environments. INBIO:_000091 natural enemy enemy An organism that is a predator, consumer, parasite, parasitoid or pathogen of another organism. INBIO:_000092 human disturbance anthropogenic disturbance disturbance brought about by human activity INBIO:_000093 Chase LeCroy, orcid.org/0000-0002-1338-9436 From http://purl.dataone.org/odo/ECSO_00000311. This class should be incorporated into ENVO. WordNet a group of organisms of the same species inhabiting a given area http://www.physicalgeography.net/fundamentals/9d.html population A population comprises all the individuals of a given species in a specific area or region at a certain time. INBIO:_000094 from https://en.wikipedia.org/wiki/Genetic_diversity genetic diversity Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species, it ranges widely from the number of species to differences within species and can be attributed to the span of survival for a species. It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary. INBIO:_000134 invasion rate Invasion rate refers to the speed or frequency at which an invasive species spreads into new areas within a given time frame. It is a critical measure in invasion biology to assess the potential impact and management needs of invasive species. INBIO:_000135 population dynamics Population dynamics in invasion biology refers to the study of how invasive species populations change over time and space, affected by births, deaths, and migration rates. INBIO:_000136 generalist herbivore A generalist herbivore is an organism that feeds on a wide variety of plant species, rather than specializing in a particular type of plant. In the context of invasion biology, generalist herbivores can have significant impacts on ecosystems by consuming native and non-native plant species, potentially facilitating the spread of invasive plants. INBIO:_000137 ecosystem dynamics Ecosystem dynamics cover the changes and processes within ecosystems driven by both native and invasive species, including nutrient flows and energy cycles. INBIO:_000138 invasive weed An invasive weed is a type of plant that is not native to a specific location and has a tendency to spread, which can cause damage to the environment, human economy, or human health. INBIO:_000139 native vegetation Native vegetation refers to plant species that are indigenous to a region, playing a critical role in maintaining ecological balance and resisting invasive species. INBIO:_000140 biotic acceptance Biotic acceptance is a concept in invasion biology that suggests that ecosystems with high native species diversity are more likely to accept invasive species, as opposed to resisting them. INBIO:_000141 native biodiversity Native biodiversity in invasion biology refers to the variety and variability of native species within an ecological community, crucial for ecosystem resilience and stability. INBIO:_000142 original community Original community refers to the assemblage of native species and their interactions within a specific ecosystem prior to the introduction of alien species. INBIO:_000143 ecological disruption Ecological disruption involves significant changes to ecosystem structure and function due to invasive species, leading to loss of biodiversity and altered ecosystem services. INBIO:_000144 detritivore A detritivore is an organism that feeds on dead organic material, particularly plant detritus, playing a crucial role in the decomposition process and nutrient cycling within ecosystems. INBIO:_000145 nutrient cycling Nutrient cycling examines how invasive species can alter the rates of nutrient intake, recycling, and distribution within an ecosystem. INBIO:_000146 invasion biology Invasion biology is the study of the causes and consequences of the introduction of species to new environments, where they establish, spread, and have impacts on native ecosystems and biodiversity. INBIO:_000147 pathways of species introduction Pathways of species introduction are the routes through which non-native species are introduced into new environments, including natural dispersal and human-related activities. INBIO:_000148 fire frequency Fire frequency refers to the rate at which fires occur in a given area over a specified period of time. In the context of invasion biology, it is an important factor influencing the dynamics of ecosystems, particularly in how it affects the establishment and spread of invasive species. INBIO:_000149 species survival Species survival in invasion biology refers to the capability of native or invasive species to maintain populations under environmental pressures and competitive interactions. INBIO:_000150 invasion event An invasion event refers to the occurrence of a species entering and establishing itself in a new ecosystem, potentially causing ecological impacts. INBIO:_000151 manual removal Manual removal refers to the physical extraction of invasive species by human effort, often used as a management strategy in invasion biology to control or eradicate non-native species from an ecosystem. INBIO:_000152 invasive species populations Invasive species populations in invasion biology refer to the groups of non-native organisms that establish, proliferate, and expand across new territories, often impacting local ecosystems. INBIO:_000153 dominance Dominance refers to the ability of an invasive species to exert control over a community by outcompeting native species for resources, thereby altering community dynamics and ecosystem processes. INBIO:_000154 native species decline Native species decline in invasion biology examines the decrease in native species populations due to factors such as habitat loss, competition from invasive species, and environmental changes. INBIO:_000155 community resilience Community resilience refers to the ability of a community of organisms to withstand, recover, and adapt to the impacts of invasive species, maintaining its structure, function, and dynamics. INBIO:_000156 ecosystem stability Ecosystem stability in invasion biology refers to the ability of an ecosystem to maintain its structure and function in the face of external stressors, including the introduction and spread of invasive species. INBIO:_000157 community study A community study refers to the examination and analysis of the interactions, dynamics, and characteristics of a community of organisms, particularly focusing on the impact and role of invasive species within that community. INBIO:_000158 species interactions Species interactions in invasion biology involve the various ways species influence each other within an ecosystem, including competition, predation, parasitism, and mutualism, which can be significantly altered by invasive species. INBIO:_000159 invasion process The invasion process refers to the sequence of events and mechanisms through which non-native species establish, spread, and impact new environments, often leading to ecological changes. INBIO:_000160 local ecosystems Local ecosystems in invasion biology refer to specific ecological communities within a defined geographical area, each with unique interactions and susceptibilities to the impacts of invasive species. INBIO:_000161 invasive plant An invasive plant is a species of plant that is not native to a specific location and has a tendency to spread, which can cause damage to the environment, human economy, or human health. INBIO:_000162 host availability Host availability refers to the presence and accessibility of suitable hosts for a species, particularly in the context of invasive species and their ability to establish and spread in a new environment. INBIO:_000163 species distribution Species distribution in invasion biology studies the geographical spread of species, particularly how invasive species expand beyond their native ranges, influencing biodiversity and ecosystem structure. INBIO:_000164 native ecosystems Native ecosystems in invasion biology are those ecosystems that have developed naturally without human intervention and are characterized by well-established native species populations and ecological processes. INBIO:_000165 species number Species number refers to the count of distinct species present in a given area or ecosystem, often used as a measure of biodiversity and an indicator of ecological health, particularly in the context of invasion biology where it can reflect the impact of invasive species on native biodiversity. INBIO:_000166 ecosystem diversity The diversity of ecosystems refers to the range of different ecosystems found within a specific geographic area, each with unique structures, species compositions, and ecological functions, which can be impacted variably by invasive species. INBIO:_000167 mutualistic interaction A mutualistic interaction is a type of symbiosis where two or more species interact in a way that is beneficial to all involved parties. In the context of invasion biology, mutualistic interactions can influence the success and impact of invasive species by providing them with advantages such as increased resources, protection, or dispersal opportunities. INBIO:_000168 species coexistence Species coexistence in invasion biology examines how different species live together in the same habitat, focusing on the mechanisms that enable competing species to coexist and how these mechanisms are disrupted by invasive species. INBIO:_000171 invasion pattern Invasion pattern refers to the specific sequence or manner in which an invasive species spreads and establishes itself in a new environment. It encompasses the stages of introduction, establishment, and spread, and is influenced by various ecological, biological, and environmental factors. INBIO:_000172 dispersal mechanisms Insight into dispersal mechanisms in invasion biology involves understanding the various ways invasive species spread across landscapes, including natural dispersal processes like wind and water, and anthropogenic factors such as global trade. alsayed.algergawy@uni-jena.de 1.2 Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has part a core relation that holds between a whole and its part unfolds in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in this process has participant this input material (or this output material) Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. http://purl.obolibrary.org/obo/obi.owl http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant a relation between a process and a continuant, in which the continuant is somehow involved in the process this apple has quality this red color A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has quality a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity this rat is located in this cage Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime http://www.obofoundry.org/ro/#OBO_REL:located_in located in a relation between two independent continuants, the target and the location, in which the target is entirely within the location overlaps Chris Mungall surrounded by This relation acts as a join point with BSPO Chris Mungall adjacent to x adjacent to y if and only if x and y share a boundary. Chris Mungall ends Chris Mungall consumes has input Chris Mungall produces has output Chris Mungall output of Chris Mungall determines has increased levels of license https://creativecommons.org/licenses/by-nc-sa/4.0/ Birgitta König-Ries birgitta.koenig-ries@uni-jena.de https://creativecommons.org/licenses/by-nc-sa/4.0/ Invasion Biology Ontology Hrishikesh Jadhav jadhav02@ads.uni-passau.de Alsayed Algergawy alsayed.algergawy@uni-jena.de Merle Gänßinger merle.gaenssinger@uni-jena.de Tina Heger t.heger@tum.de https://creativecommons.org/licenses/by-nc-sa/4.0/ https://creativecommons.org/licenses/by-nc-sa/4.0/ The Invasion Biology Ontology (INBIO) contains terms and concepts relevant in the field of invasion biology, which is a research area dealing with the translocation, establishment, spread, impact and management of species outside of their native ranges, where they are called non-native or alien species. This first version of the ontology covers terms and concepts needed to describe twelve major invasion hypotheses building the hierarchical hypothesis network (see also Jeschke JM, Heger T (Eds) (2018) Invasion Biology: Hypotheses and Evidence. CABI, Wallingford, UK). 1.1 1.2