None SEOnt If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole 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 BFO:0000050 external quality part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. a core relation that holds between a whole and its part 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 BFO:0000051 external quality has_part has_part We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. has part has part has_part Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. PATOC:CJM preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in 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 site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process A duck swimming in a pond is partially surrounded by air and partially surrounded by water. x partially_surrounded_by y if and only if (1) x is adjacent to y and for the region r that is adjacent to x, r partially overlaps y (2) the shared boundary between x and y occupies a non-trivial proportion of the outermost boundary of x Definition modified from 'surrounded by'. partially_surrounded_by This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes inverse of the relation 'denotes' Person: Jie Zheng, Chris Stoeckert, Mike Conlon denoted by inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process 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. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role 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 role of this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence 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 has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) 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 is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_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 this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) 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 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 derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location 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 location_of location of contained in 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 contained in contains contains located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location 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 located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. has ligand dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes David Osumi-Sutherland o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps true true x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. only in taxon x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. in taxon A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' 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 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)". RO_0000053 some (RO_0000054 only ?Y) capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of true true x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in actively participates in 'heart development' has active participant some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent has active participant obsolete has active participant true x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x Chris Mungall surrounded by surrounded by A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO Chris Mungall adjacent to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. inverse of surrounded by Chris Mungall surrounds Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to inverse of ends with Chris Mungall ends x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by ends with x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y Chris Mungall ends with process that occurs in has end location p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. Chris Mungall produces has output A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. c involved in regulation of p if c enables 'p' and p' causally upstream of p acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. Chris Mungall results_in_developmental_progression_of results in developmental progression of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) Chris Mungall GOC:mtg_berkeley_2013 results_in_formation_of results in formation of Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. Pier Buttigieg adapted for living in A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. has habitat has habitat cjm cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall inheres in part of true A relationship that holds via some environmental process evolutionarily related to A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions ecologically related to A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex 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. Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part of structure that is capable of true true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of involved in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member inverse of has input Chris Mungall input of inverse of has output Chris Mungall output of Chris Mungall formed as result of A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location Chris Mungall This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some 'p' and p' regulates some p c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in enables activity in is active in true true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos A relationship that holds between two entities in which the processes executed by the two entities are causally connected. 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 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. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected. An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Chris Mungall Vasundra Touré molecularly controls activity directly regulates activity of directly regulates activity of molecularly controls Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly inhibits molecularly decreases activity of activity directly negatively regulates activity of directly negatively regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly activates molecularly increases activity of activity directly positively regulates activity of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. Chris Mungall composed primarily of p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true true Chris Mungall is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities causal relation between material entities A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future Chris Mungall determined by (system to material entity) Chris Mungall Pier Buttigieg Chris Mungall Pier Buttigieg determined by inverse of determined by Chris Mungall determines (material entity to system) determines s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. Chris Mungall determined by part of true Chris Mungall causally influenced by (entity-centric) causally influenced by (material entity to material entity) causally influenced by Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). Chris Mungall Vasundra Touré causally influences (entity-centric) causally influences (material entity to material entity) causally influences Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates 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 A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' Inverse of 'causal agent in' has causal agent process has causal agent A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. related via dependence to Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. 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 a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel produced by Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. Vasundra Touré regulates activity of has start date has end date A planned process in which water is artificially supplied to plant or soil to sustain plants. irrigation irrigation process A planned process in which water is artificially supplied to plant or soil to sustain plants. https://en.wikipedia.org/wiki/Irrigation www.dictionary.com/browse/irrigation A role that inheres in a water body that is realised in an irrigation process where water is transported from that water body to the target of the irrigation process. irrigation water source role A water body from which water is taken during an irrigation process and transported to the target of the irrigation process. irrigation source A plant anatomical entity that is defined to mean plants or parts of plant capable of and intended for producing or reproducing entire plants. plant reproductive material A plant anatomical entity that is defined to mean plants or parts of plant capable of and intended for producing or reproducing entire plants. http://ec.europa.eu/dgs/health_food-safety/pressroom/docs/proposal_aphp_en.pdf A plan specification which describes how water is applied to plants or soil. irrigation method Organism used to pull agricultural implements. draught animal working animal draft animal A mobile machine specifically designed to deliver a high tractive effort at slow speeds, and mainly used for the purposes of hauling a trailer or machinery used in agriculture or construction. tractor A mobile machine specifically designed to deliver a high tractive effort at slow speeds, and mainly used for the purposes of hauling a trailer or machinery used in agriculture or construction. https://en.wikipedia.org/wiki/Tractor Plant material remaining on the field ground after harvesting, including leaves, stalks, roots. crop residue Plant material remaining on the field ground after harvesting, including leaves, stalks, roots. https://stats.oecd.org/glossary/detail.asp?ID=480 two or more crop plants planted in a line. row A site which is located between two rows of crop plants. interrow An equipment that is used during an irrigation process. irrigation equipment A site within which an agricultural experimental process is conducted This should be harmonized with statistical plot designs, perhaps with STATO plot agricultural experimental plot A site within which an agricultural experimental process is conducted http://www.fao.org/wairdocs/ilri/x5546e/x5546e0a.htm Distance quality that represents the distance between two plots. plot spacing Distance between two rows. The distance of a whole plant distance between rows interrow row spacing space between rows distance between plants Average distance between plants in a same row. The distance of a row space between plants in row distance between rows A process during which some material is applied to a subject treatment A process during which some material is applied to a subject http://www.fao.org/wairdocs/ilri/x5546e/x5546e0a.htm A crop is any cultivated plant, fungus, or alga that is harvested for food, clothing, livestock,fodder, biofuel, medicine, or other uses crop A crop is any cultivated plant, fungus, or alga that is harvested for food, clothing, livestock,fodder, biofuel, medicine, or other uses https://en.wikipedia.org/wiki/Crop The landform refers to the shape of the land surface in the area in which the agronomic trial site is located. higher-level landform The landform refers to the shape of the land surface in the area in which the agronomic trial site is located. http://www.fao.org/docrep/019/a0541e/a0541e.pdf Description of the geomorphology of the immediate surroundings of the experimental site. agronomic land element Description of the geomorphology of the immediate surroundings of the experimental site. http://www.fao.org/docrep/019/a0541e/a0541e.pdf A factor of an experiment is a controlled independent variable; a variable whose levels are set by the experimenter. A factor is a general type or category of treatments. Different treatments constitute different levels of a factor. experimental factor A factor of an experiment is a controlled independent variable; a variable whose levels are set by the experimenter. A factor is a general type or category of treatments. Different treatments constitute different levels of a factor. http://www.stat.yale.edu/Courses/1997-98/101/expdes.htm A plan specification that states how treatments are allocated to the experimental units during an agronomic trial. It refers to the conceptual framework within which the experiment is conducted. agronomic experimental design A plan specification that states how treatments are allocated to the experimental units during an agronomic trial. It refers to the conceptual framework within which the experiment is conducted. http://www.simplypsychology.org/experimental-designs.html https://en.wikipedia.org/wiki/Design_of_experiments https://www.okstate.edu/ag/agedcm4h/academic/aged5980a/5980/newpage2.htm Shape quality that refers to the general shape of a slope in both vertical and horizontal directions. slope form slope shape Shape quality that refers to the general shape of a slope in both vertical and horizontal directions. FAO, 1990 A planned process in which a procedure is carried out to support, refute, or validate a hypothesis. This class is relevant to more than the agronomy domain. It should be replaced by a class in a more general ontology of experiments trial experiment A planned process in which a procedure is carried out to support, refute, or validate a hypothesis. https://en.wikipedia.org/wiki/Experiment An experiment in which a scientific method is implemented for testing certain agricultural phenomena. agronomic experiment agricultural experiment agricultural implement 1 An agricultural experiment involving the prolonged growing of a single crop. continuous crop experiment continuous mono-cropping experiment monoculture experiment mono-cropping experiment mono-cropping experiment Richard Ostler A role that inheres in an animal that is kept by humans and trained to perform tasks. draft animal draught animal working animal draft animal role A role that inheres in a human to power an implement. human power role A planned process which occurs during an agricultural experiment. agricultural process 2 An agricultural experiment during which at least two different crops are grown at the same time. inter-cropping experiment entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant 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. 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. 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 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]) 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]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant continuant 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 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]) 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]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) 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]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) http://purl.obolibrary.org/obo/bfo/axiom/017-002 b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) 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]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) http://purl.obolibrary.org/obo/bfo/axiom/083-003 p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] quality sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella 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. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] site object gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. 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. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. 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. 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]) 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]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity 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]) 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]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] immaterial entity anatomical structure material anatomical entity Material anatomical entity that is a member of an individual species or is a viral or viroid particle. organism or virus Melissa Haendel 9/18/11 organism or virus or viroid Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. electron Elektron beta beta(-) beta-particle e e(-) e- negatron electron electron ChEBI electron IUPAC electron KEGG_COMPOUND Elektron ChEBI beta IUPAC beta(-) ChEBI beta-particle IUPAC e IUPAC e(-) UniProt e- KEGG_COMPOUND negatron IUPAC A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water. inorganic acids mineral acid mineral acids inorganic acid inorganic acids ChEBI mineral acid ChEBI mineral acids ChEBI Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). gas molecular entities gaseous molecular entities gaseous molecular entity gas molecular entity gas molecular entities ChEBI gaseous molecular entities ChEBI gaseous molecular entity ChEBI electron donor A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity. Acceptor A Akzeptor Hydrogen-acceptor Oxidized donor accepteur acceptor Acceptor KEGG_COMPOUND A KEGG_COMPOUND Akzeptor ChEBI Hydrogen-acceptor KEGG_COMPOUND Oxidized donor KEGG_COMPOUND accepteur ChEBI An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. WATER Water oxidane water BOUND WATER H2O HOH Wasser [OH2] acqua agua aqua dihydridooxygen dihydrogen oxide eau hydrogen hydroxide water WATER PDBeChem Water KEGG_COMPOUND oxidane IUPAC water IUPAC BOUND WATER PDBeChem H2O KEGG_COMPOUND H2O UniProt HOH ChEBI Wasser ChEBI [OH2] IUPAC acqua ChEBI agua ChEBI aqua ChEBI dihydridooxygen IUPAC dihydrogen oxide IUPAC eau ChEBI hydrogen hydroxide ChEBI dioxygen A monoatomic monoanion resulting from the addition of an electron to any halogen atom. halide ions HX Halide a halide anion halide anions halide(1-) halides halogen anion halide anion halide ions IUPAC HX KEGG_COMPOUND Halide KEGG_COMPOUND a halide anion UniProt halide anions ChEBI halide(1-) ChEBI halides ChEBI halogen anion ChEBI hydridooxygenate(1-) hydroxide oxidanide HO- HYDROXIDE ION Hydroxide ion OH(-) OH- hydroxide hydridooxygenate(1-) IUPAC hydroxide IUPAC oxidanide IUPAC HO- KEGG_COMPOUND HYDROXIDE ION PDBeChem Hydroxide ion KEGG_COMPOUND OH(-) IUPAC OH- KEGG_COMPOUND A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. carbon dioxide A mononuclear parent hydride consisting of covalently bonded hydrogen and chlorine atoms. Hydrogen chloride chlorane chloridohydrogen hydrogen chloride Chlorwasserstoff HCl Hydrochloride Hydrogenchlorid Wasserstoffchlorid [HCl] chlorure d'hydrogene cloruro de hidrogeno hydrochloric acid hydrogen chloride Hydrogen chloride KEGG_COMPOUND chlorane IUPAC chloridohydrogen IUPAC hydrogen chloride IUPAC Chlorwasserstoff ChEBI HCl KEGG_COMPOUND Hydrochloride KEGG_COMPOUND Hydrogenchlorid ChEBI Wasserstoffchlorid ChEBI [HCl] IUPAC chlorure d'hydrogene ChEBI cloruro de hidrogeno ChEBI hydrochloric acid ChemIDplus A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity. Donor Donator donneur donor Donor KEGG_COMPOUND Donator ChEBI donneur ChEBI A halide anion formed when chlorine picks up an electron to form an an anion. Chloride chloride chloride(1-) CHLORIDE ION Chloride ion Chloride(1-) Chlorine anion Cl(-) Cl- chloride Chloride KEGG_COMPOUND chloride IUPAC chloride UniProt chloride(1-) IUPAC CHLORIDE ION PDBeChem Chloride ion KEGG_COMPOUND Chloride(1-) ChemIDplus Chlorine anion NIST_Chemistry_WebBook Cl(-) IUPAC Cl- KEGG_COMPOUND An elemental molecule consisting of two trivalently-bonded nitrogen atoms. dinitrogen N#N N2 Nitrogen molecular nitrogen dinitrogen dinitrogen IUPAC N#N ChEBI N2 IUPAC N2 KEGG_COMPOUND N2 UniProt Nitrogen KEGG_COMPOUND molecular nitrogen ChEBI hydrogen halide hydrogen halides HX hydrogen halides hydrogen halide hydrogen halide IUPAC hydrogen halides IUPAC HX UniProt hydrogen halides ChEBI alkali metals Alkalimetall Alkalimetalle alkali metal metal alcalin metal alcalino metales alcalinos metaux alcalins alkali metal atom alkali metals IUPAC Alkalimetall ChEBI Alkalimetalle ChEBI alkali metal ChEBI metal alcalin ChEBI metal alcalino ChEBI metales alcalinos ChEBI metaux alcalins ChEBI A monoatomic or polyatomic species having one or more elementary charges of the electron. Anion anion Anionen aniones anions anion Anion ChEBI anion ChEBI anion IUPAC Anionen ChEBI aniones ChEBI anions IUPAC A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base). Base base Base1 Base2 Basen Nucleobase bases base Base ChEBI base ChEBI base IUPAC Base1 KEGG_COMPOUND Base2 KEGG_COMPOUND Basen ChEBI Nucleobase KEGG_COMPOUND bases ChEBI carbon oxide chloride salts chlorides chloride salt chloride salts ChEBI chlorides ChEBI chlorine 17Cl Chlor Cl chlore chlorine chlorum cloro chlorine atom chlorine IUPAC 17Cl IUPAC Chlor ChEBI Cl IUPAC chlore ChEBI chlorine ChEBI chlorum ChEBI cloro ChEBI A halogen molecular entity containing one or more atoms of chlorine. chlorine molecular entity An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group). cofactor cofactors cofactor cofactor IUPAC cofactors IUPAC Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet molecular entity molecular entity IUPAC entidad molecular IUPAC entidades moleculares IUPAC entite moleculaire IUPAC molecular entities IUPAC molekulare Entitaet ChEBI monoatomic anions monoatomic anion monoatomic anions ChEBI monoatomic cations monoatomic cation monoatomic cations ChEBI A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chemical entity chemical entity UniProt A role played by the molecular entity or part thereof within a biological context. biological function biological role biological function ChEBI A defined linked collection of atoms or a single atom within a molecular entity. group Gruppe Rest groupe grupo grupos group group IUPAC Gruppe ChEBI Rest ChEBI groupe IUPAC grupo IUPAC grupos IUPAC halogen molecular entity halogen compounds halogen molecular entities halogen molecular entity halogen molecular entity ChEBI halogen compounds ChEBI halogen molecular entities ChEBI halogen halogens Halogene group 17 elements group VII elements halogene halogenes halogeno halogenos halogen halogen IUPAC halogens IUPAC Halogene ChEBI group 17 elements ChEBI group VII elements ChEBI halogene ChEBI halogenes ChEBI halogeno ChEBI halogenos ChEBI Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). hydroxides inorganic anions inorganic anion inorganic anions ChEBI A molecular entity that contains no carbon. anorganische Verbindungen inorganic compounds inorganic entity inorganic molecular entities inorganics inorganic molecular entity anorganische Verbindungen ChEBI inorganic compounds ChEBI inorganic entity ChEBI inorganic molecular entities ChEBI inorganics ChEBI anorganisches Salz inorganic salts inorganic salt anorganisches Salz ChEBI inorganic salts ChEBI A salt is an assembly of cations and anions. salt Salz Salze ionic compound ionic compounds sal sales salts sel sels salt salt IUPAC Salz ChEBI Salze ChEBI ionic compound ChEBI ionic compounds ChEBI sal ChEBI sales ChEBI salts ChEBI sel ChEBI sels ChEBI monoatomic ions monoatomic ion monoatomic ions ChEBI A molecular entity having a net electric charge. Ion ion Ionen iones ions ion Ion ChEBI ion ChEBI ion IUPAC Ionen ChEBI iones ChEBI ions ChEBI Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. metabolite metabolites primary metabolites secondary metabolites metabolite metabolite IUPAC metabolites ChEBI primary metabolites ChEBI secondary metabolites ChEBI a metal cation metal cations metal cation a metal cation UniProt metal cations ChEBI A molecule all atoms of which have the same atomic number. homoatomic molecule homoatomic molecules elemental molecule homoatomic molecule ChEBI homoatomic molecules ChEBI Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule Molekuel molecula molecules neutral molecular compounds molecule molecule IUPAC Molekuel ChEBI molecula IUPAC molecules IUPAC neutral molecular compounds IUPAC monoatomic monocations monovalent inorganic cations monoatomic monocation monoatomic monocations ChEBI monovalent inorganic cations ChEBI nitrogen 7N N Stickstoff azote nitrogen nitrogeno nitrogen atom nitrogen IUPAC 7N IUPAC N IUPAC Stickstoff ChEBI azote IUPAC nitrogen ChEBI nitrogeno ChEBI nonmetal Nichtmetall Nichtmetalle no metal no metales non-metal non-metaux nonmetal nonmetals nonmetal atom nonmetal IUPAC Nichtmetall ChEBI Nichtmetalle ChEBI no metal ChEBI no metales ChEBI non-metal ChEBI non-metaux ChEBI nonmetal ChEBI nonmetals ChEBI An oxide in which the oxygen atom is bonded to a carbon atom. organic oxide An oxide is a chemical compound of oxygen with other chemical elements. oxide oxides oxide oxide ChEBI oxides ChEBI oxygen 8O O Sauerstoff oxigeno oxygen oxygene oxygen atom oxygen IUPAC 8O IUPAC O IUPAC Sauerstoff ChEBI oxigeno ChEBI oxygen ChEBI oxygene ChEBI oxygen molecular entity oxygen molecular entities oxygen molecular entity oxygen molecular entity ChEBI oxygen molecular entities ChEBI sodium 11Na Na Natrium natrium sodio sodium sodium atom sodium IUPAC 11Na IUPAC Na IUPAC Natrium ChemIDplus natrium IUPAC sodio ChemIDplus sodium ChEBI An inorganic chloride salt having sodium(1+) as the counterion. sodium chloride sodium compounds sodium molecular entities sodium molecular entity sodium compounds ChEBI sodium molecular entities ChEBI Any alkali metal salt having sodium(1+) as the cation. Natriumsalz Natriumsalze sodium salts sodium salt Natriumsalz ChEBI Natriumsalze ChEBI sodium salts ChEBI Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions. micronutrients trace elements micronutrient micronutrients ChEBI trace elements ChEBI carbon 6C C Carbon Kohlenstoff carbon carbone carbonium carbono carbon atom carbon IUPAC 6C IUPAC C IUPAC C KEGG_COMPOUND Carbon KEGG_COMPOUND Kohlenstoff ChEBI carbon ChEBI carbone ChEBI carbonium ChEBI carbono ChEBI A monoatomic monocation obtained from sodium. sodium cation sodium(1+) sodium(1+) ion sodium(I) cation Na(+) Na+ SODIUM ION sodium(1+) sodium cation IUPAC sodium(1+) IUPAC sodium(1+) ion IUPAC sodium(I) cation IUPAC Na(+) IUPAC Na(+) UniProt Na+ KEGG_COMPOUND SODIUM ION PDBeChem aquahydrogen(1+) oxidanium oxonium trihydridooxygen(1+) H3O(+) Hydronium cation Hydronium ion [OH3](+) oxonium aquahydrogen(1+) IUPAC oxidanium IUPAC oxonium IUPAC trihydridooxygen(1+) IUPAC H3O(+) IUPAC Hydronium cation NIST_Chemistry_WebBook Hydronium ion ChemIDplus [OH3](+) MolBase diazynediium HNNH(2+) [HNNH](2+) diazynediium diazynediium IUPAC HNNH(2+) IUPAC [HNNH](2+) ChEBI diazynium HN2+ N#NH(+) diazynium diazynium IUPAC HN2+ NIST_Chemistry_WebBook N#NH(+) IUPAC Intended use of the molecular entity or part thereof by humans. application A particle not known to have substructure. elementary particle elementary particles fundamental particle elementary particle IUPAC elementary particles ChEBI A monoatomic entity is a molecular entity consisting of a single atom. atomic entity monoatomic entities monoatomic entity atomic entity ChEBI monoatomic entities ChEBI inorganic hydrides inorganic hydride inorganic hydrides ChEBI Any substituent group which does not contain carbon. inorganic groups inorganic group inorganic groups ChEBI A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom atome atomo atoms atomus element elements atom atom IUPAC atome IUPAC atomo IUPAC atoms ChEBI atomus ChEBI element ChEBI elements ChEBI A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. nucleus Atomkern Kern noyau noyau atomique nuclei nucleo nucleo atomico nucleus atomi atomic nucleus nucleus IUPAC Atomkern ChEBI Kern ChEBI noyau IUPAC noyau atomique ChEBI nuclei ChEBI nucleo IUPAC nucleo atomico ChEBI nucleus atomi ChEBI Heavy nuclear particle: proton or neutron. nucleon Nukleon Nukleonen nucleons nucleon nucleon IUPAC nucleon IUPAC Nukleon ChEBI Nukleonen ChEBI nucleons ChEBI A molecular entity all atoms of which have the same atomic number. homoatomic entity homoatomic molecular entities homoatomic molecular entity elemental molecular entity homoatomic entity ChEBI homoatomic molecular entities ChEBI homoatomic molecular entity ChEBI elemental oxygen diatomic oxygen diatomic nitrogen elemental nitrogen A nutrient is a food component that an organism uses to survive and grow. nutrients nutrient nutrients ChEBI A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. heteroorganic entities organoelement compounds heteroorganic entity heteroorganic entities ChEBI organoelement compounds ChEBI Any material that can be ingested by an organism. food A molecular entity containing one or more atoms of an alkali metal. alkali metal molecular entities alkali metal molecular entity alkali metal molecular entities ChEBI Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth. pnictogens group 15 elements group V elements nitrogenoideos nitrogenoides pnictogene pnictogenes pnictogen pnictogens IUPAC group 15 elements ChEBI group V elements ChEBI nitrogenoideos ChEBI nitrogenoides ChEBI pnictogene ChEBI pnictogenes ChEBI A p-block molecular entity containing any pnictogen. pnictogen molecular entity pnictogen molecular entities pnictogen molecular entity pnictogen molecular entity ChEBI pnictogen molecular entities ChEBI Any p-block element belonging to the group 16 family of the periodic table. chalcogen chalcogens Chalkogen Chalkogene anfigeno anfigenos calcogeno calcogenos chalcogene chalcogenes group 16 elements group VI elements chalcogen chalcogen IUPAC chalcogens IUPAC Chalkogen ChEBI Chalkogene ChEBI anfigeno ChEBI anfigenos ChEBI calcogeno ChEBI calcogenos ChEBI chalcogene ChEBI chalcogenes ChEBI group 16 elements ChEBI group VI elements ChEBI Any p-block molecular entity containing a chalcogen. chalcogen molecular entity chalcogen compounds chalcogen molecular entities chalcogen molecular entity chalcogen molecular entity ChEBI chalcogen compounds ChEBI chalcogen molecular entities ChEBI group 14 elements carbon group element carbon group elements carbonoides cristallogene cristallogenes group IV elements carbon group element atom group 14 elements IUPAC carbon group element ChEBI carbon group elements ChEBI carbonoides ChEBI cristallogene ChEBI cristallogenes ChEBI group IV elements ChEBI An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. main group elements Hauptgruppenelement Hauptgruppenelemente main group element main group element atom main group elements IUPAC Hauptgruppenelement ChEBI Hauptgruppenelemente ChEBI main group element ChEBI A hydracid is a compound which contains hydrogen that is not bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). hydracid hydracids hydracid hydracid IUPAC hydracids ChEBI monoatomic monoanions monoatomic monoanion monoatomic monoanions ChEBI elemental chlorine atomic chlorine monoatomic chlorine atomic chlorine ChEBI monoatomic halogens monoatomic halogen monoatomic halogens ChEBI elemental halogen elemental halogens elemental halogen elemental halogen ChEBI elemental halogens ChEBI elemental pnictogen elemental pnictogens elemental pnictogen elemental pnictogen ChEBI elemental pnictogens ChEBI alkali metal cations alkali metal cation alkali metal cations ChEBI An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity. elemental metal elemental metals metal element metal elements metals metal atom elemental metal ChEBI elemental metals ChEBI metal element ChEBI metal elements ChEBI metals ChEBI s-block element s-block elements s-block element atom s-block element ChEBI s-block elements ChEBI Any main group element atom belonging to the p-block of the periodic table. p-block element p-block elements p-block element atom p-block element ChEBI p-block elements ChEBI A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. main group compounds main group molecular entities main group molecular entity main group compounds ChEBI main group molecular entities ChEBI carbon group molecular entity carbon group molecular entities carbon group molecular entity carbon group molecular entity ChEBI carbon group molecular entities ChEBI A main group molecular entity containing one or more atoms of any noble gas. noble gas molecular entity hydrogen compounds hydrogen molecular entities hydrogen molecular entity hydrogen compounds ChEBI hydrogen molecular entities ChEBI An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element. s-block molecular entity s-block compounds s-block molecular entities s-block molecular entity s-block molecular entity ChEBI s-block compounds ChEBI s-block molecular entities ChEBI A main group molecular entity that contains one or more atoms of a p-block element. p-block compounds p-block molecular entities p-block molecular entitiy p-block molecular entity p-block compounds ChEBI p-block molecular entities ChEBI p-block molecular entitiy ChEBI helium molecular entity Hydrides are chemical compounds of hydrogen with other chemical elements. hydrides oxygen hydride hydrides of oxygen oxygen hydrides oxygen hydride oxygen hydride ChEBI hydrides of oxygen ChEBI oxygen hydrides ChEBI A macromolecule formed by a living organism. biomacromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. macromolecule macronutrient halide salts halides halide salt halide salts ChEBI halides ChEBI nitrogen hydrides nitrogen hydride nitrogen hydrides ChEBI alkali metal salts alkali metal salt alkali metal salts ChEBI pnictogen hydride pnictogen hydrides pnictogen hydride pnictogen hydride ChEBI pnictogen hydrides ChEBI inorganic chloride salt inorganic chloride salts inorganic chlorides inorganic chloride inorganic chloride salt ChEBI inorganic chloride salts ChEBI inorganic chlorides ChEBI Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin). leptons lepton leptons ChEBI Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy). baryons baryon baryons ChEBI Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi. fermion fermions fermion fermion IUPAC fermions ChEBI A particle smaller than an atom. subatomic particles subatomic particle subatomic particles ChEBI A subatomic particle known to have substructure (i.e. consisting of smaller particles). composite particles composite particle composite particles ChEBI Hadron is a subatomic particle which experiences the strong force. hadrons hadron hadrons ChEBI A nucleus or any of its constituents in any of their energy states. nuclear particle nuclear particle nuclear particle IUPAC Any molecular entity consisting of more than one atom. polyatomic entities polyatomic entity polyatomic entities ChEBI monoanions monoanion monoanions ChEBI chalcogen hydride chalcogen hydrides chalcogen hydride chalcogen hydride ChEBI chalcogen hydrides ChEBI argon molecular entity inorganic ions inorganic ion inorganic ions ChEBI inorganic cations inorganic cation inorganic cations ChEBI A monoatomic or polyatomic species having one or more elementary charges of the proton. Cation cation Kation Kationen cationes cations cation Cation KEGG_COMPOUND cation ChEBI cation IUPAC Kation ChEBI Kationen ChEBI cationes ChEBI cations ChEBI An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound organochalcogen compounds organochalcogen compound organochalcogen compound ChEBI organochalcogen compounds ChEBI An organochalcogen compound containing at least one carbon-oxygen bond. organooxygen compound organooxygen compounds organooxygen compound organooxygen compound ChEBI organooxygen compounds ChEBI mononuclear parent hydrides mononuclear hydride mononuclear hydrides mononuclear parent hydride mononuclear parent hydrides IUPAC mononuclear hydride ChEBI mononuclear hydrides IUPAC elemental sodium An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid). Acid acid Saeure Saeuren acide acido acids acid Acid KEGG_COMPOUND acid IUPAC Saeure ChEBI Saeuren ChEBI acide IUPAC acido ChEBI acids ChEBI A molecular entity consisting of two or more chemical elements. chemical compound heteroatomic molecular entities heteroatomic molecular entity chemical compound ChEBI heteroatomic molecular entities ChEBI Any heteroatomic molecular entity that is a chemical compound of halogen with other chemical elements. halides halide halides ChEBI inorganic sodium salts inorganic sodium salt inorganic sodium salts ChEBI A molecular entity capable of donating a hydron to an acceptor (Bronsted base). Bronsted acid Bronsted-Saeure acide de Bronsted donneur d'hydron hydron donor Bronsted acid Bronsted acid IUPAC Bronsted-Saeure ChEBI acide de Bronsted IUPAC donneur d'hydron IUPAC hydron donor IUPAC A molecular entity capable of accepting a hydron from a donor (Bronsted acid). Bronsted base Bronsted-Base accepteur d'hydron base de Bronsted hydron acceptor Bronsted base Bronsted base IUPAC Bronsted-Base ChEBI accepteur d'hydron IUPAC base de Bronsted IUPAC hydron acceptor IUPAC HYDROXY GROUP hydroxy hydroxy group -OH hydroxyl hydroxyl group hydroxy group HYDROXY GROUP PDBeChem hydroxy IUPAC hydroxy group UniProt -OH IUPAC hydroxyl ChEBI hydroxyl group ChEBI In general, a mineral is a chemical substance that is normally crystalline formed and has been formed as a result of geological processes. The term also includes metamict substances (naturally occurring, formerly crystalline substances whose crystallinity has been destroyed by ionising radiation) and can include naturally occurring amorphous substances that have never been crystalline ('mineraloids') such as georgite and calciouranoite as well as substances formed by the action of geological processes on bigenic compounds ('biogenic minerals'). mineral A liquid that can dissolve other substances (solutes) without any change in their chemical composition. Loesungsmittel solvant solvents solvent Loesungsmittel ChEBI solvant ChEBI solvents ChEBI A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds. polar solvent polar solvents polar solvent polar solvent IUPAC polar solvents ChEBI A polar solvent that is capable of acting as a hydron (proton) donor. protogenic solvent protic solvent protogenic solvent IUPAC protophilic solvent amphiprotic solvent hydrogen 1H H Wasserstoff hidrogeno hydrogen hydrogene hydrogen atom hydrogen IUPAC 1H IUPAC H IUPAC Wasserstoff ChEBI hidrogeno ChEBI hydrogen ChEBI hydrogene ChEBI onium compound Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families. onium cations onium cations onium ion onium ions onium cation onium cations IUPAC onium cations ChEBI onium ion ChEBI onium ions ChEBI chloranium chloronium H2Cl(+) [ClH2](+) chloronium chloranium IUPAC chloronium IUPAC H2Cl(+) IUPAC [ClH2](+) IUPAC Any molecular entity that contains carbon. organic compounds organic entity organic molecular entities organic molecular entity organic compounds ChEBI organic entity ChEBI organic molecular entities ChEBI A role is particular behaviour which a material entity may exhibit. role A role played by the molecular entity or part thereof within a chemical context. chemical role Nitrogenous compounds nitrogen compounds nitrogen molecular entities nitrogen molecular entity Nitrogenous compounds KEGG_COMPOUND nitrogen compounds ChEBI nitrogen molecular entities ChEBI A biological role played by the molecular entity or part thereof within a biochemical context. biochemical role physiological role inorganic hydroxides inorganic hydroxy compound inorganic hydroxides ChEBI A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. Chemische Substanz chemical substance Chemische Substanz ChEBI An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one. a monovalent cation monovalent inorganic cation a monovalent cation UniProt Any substance which is added to food to preserve or enhance its flavour and/or appearance. food additives food additive food additives ChEBI An organic molecular entity containing a single carbon atom (C1). one-carbon compounds one-carbon compound one-carbon compounds ChEBI Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. organic compound organic compounds organic molecules organic molecule organic compound ChEBI organic compounds ChEBI organic molecules ChEBI Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms. eukaryotic metabolites eukaryotic metabolite eukaryotic metabolites ChEBI Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals. animal metabolites animal metabolite animal metabolites ChEBI Any animal metabolite produced during a metabolic reaction in mammals. mammalian metabolites mammalian metabolite mammalian metabolites ChEBI Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus). Mus musculus metabolite Mus musculus metabolites mouse metabolites mouse metabolite Mus musculus metabolite ChEBI Mus musculus metabolites ChEBI mouse metabolites ChEBI Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae). S. cerevisiae metabolite S. cerevisiae metabolites S. cerevisiae secondary metabolite S. cerevisiae secondary metabolites Saccharomyces cerevisiae metabolites Saccharomyces cerevisiae secondary metabolites baker's yeast metabolite baker's yeast metabolites baker's yeast secondary metabolite baker's yeast secondary metabolites Saccharomyces cerevisiae metabolite S. cerevisiae metabolite ChEBI S. cerevisiae metabolites ChEBI S. cerevisiae secondary metabolite ChEBI S. cerevisiae secondary metabolites ChEBI Saccharomyces cerevisiae metabolites ChEBI Saccharomyces cerevisiae secondary metabolites ChEBI baker's yeast metabolite ChEBI baker's yeast metabolites ChEBI baker's yeast secondary metabolite ChEBI baker's yeast secondary metabolites ChEBI Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea. prokaryotic metabolites prokaryotic metabolite prokaryotic metabolites ChEBI A gas in an atmosphere that absorbs and emits radiation within the thermal infrared range, so contributing to the 'greenhouse effect'. greenhouse gases envoPolar greenhouse gas greenhouse gases ChEBI A compressed gas or liquid with a boiling point lower than room temperature which to used to propel and dispense liquids such as deodorants, insecticides, paints, etc. from aerosol cans. propellants propellant propellants ChEBI Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds. fungal metabolites fungal metabolite fungal metabolites ChEBI Any prokaryotic metabolite produced during a metabolic reaction in bacteria. bacterial metabolite Any bacterial metabolite produced during a metabolic reaction in Escherichia coli. E.coli metabolite E.coli metabolites Escherichia coli metabolites Escherichia coli metabolite E.coli metabolite ChEBI E.coli metabolites ChEBI Escherichia coli metabolites ChEBI Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens). H. sapiens metabolite H. sapiens metabolites Homo sapiens metabolite Homo sapiens metabolites human metabolite H. sapiens metabolite ChEBI H. sapiens metabolites ChEBI Homo sapiens metabolite ChEBI Homo sapiens metabolites ChEBI A food additive that is a (generally inert) gas which is used to envelop foodstuffs during packing and so protect them from unwanted chemical reactions such as food spoilage or oxidation during subsequent transport and storage. The term includes propellant gases, used to expel foods from a container. food packaging gases food packaging gas food packaging gases ChEBI A propellant that is used to expel foods from an aerosol container. food propellants food propellant food propellants ChEBI Any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants. dietary component dietary components food components food component dietary component ChEBI dietary components ChEBI food components ChEBI Any inorganic anion with a valency of one. monovalent inorganic anions monovalent inorganic anion monovalent inorganic anions ChEBI https://en.wikipedia.org/wiki/Geographic_feature macroscopic spatial feature envoPolar May appear on a map. geographic feature An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature. An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature. 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. ORCID:0000-0002-4366-3088 An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature. ORCID:0000-0002-4366-3088 A geographical feature associated with water. 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. MA:ma fluvial feature ADL:FTT A marine water body which is constitutes the majority of an astronomical body's hydrosphere. LTER:695 EcoLexicon:ocean FTT:1019 FTT:943 Geonames:H.OCN SWEETRealm:Ocean TGN:21102 https://en.wikipedia.org/wiki/Ocean Ocean ocean ocean region envoMarine envoPolar ocean LTER:695 http://129.24.124.196/vocab/vocab/index.php?tema=127&/coral-reefs Ocean NASA:earthrealm ocean Geonames:feature ocean region ADL:FTT A large expanse of saline water usually connected with an ocean. EcoLexicon:sea FTT:233 FTT:830 Geonames:H.SEA TGN:21103 https://en.wikipedia.org/wiki/Sea Sea 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. https://en.wikipedia.org/wiki/Sea Sea NASA:earthrealm sea ADL:FTT sea Geonames:feature closed sea USGS:SDTS marginal sea USGS:SDTS open sea USGS:SDTS open sound USGS:SDTS open water USGS:SDTS A geographical feature associated with water with a halinity above 30 ppt (roughly 35 g/L). ENVO ENVO:00000017 saline hydrographic feature A geographical feature associated with water with a halinity above 30 ppt (roughly 35 g/L). https://en.wikipedia.org/wiki/Salinity A lake whose water contains a considerable concentration of dissolved salts. 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. MA:ma salt lake USGS:SDTS salina USGS:SDTS A body of water or other liquid of considerable size contained in a depression on a landmass. 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. https://en.wikipedia.org/wiki/Lake 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 An vegetated area which overlaps a wetland ecosystem. WetlandRegion wetland area An vegetated area which overlaps a wetland ecosystem. https://en.wikipedia.org/wiki/Wetland WetlandRegion NASA:earthrealm An accumulation of water of varying size. 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 body 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. water body An accumulation of water of varying size. https://en.wikipedia.org/wiki/Body_of_water hydrographic feature ADL:FTT bodies of water Getty:TGN body of water ADL:FTT body of water Getty:TGN A depression which has been formed as a result of erosion by water or ice and which is low-lying, bordered by higher ground, and especially elongate. EcoLexicon:valley FTT:158 FTT:166 FTT:418 FTT:761 FTT:811 FTT:949 Geonames:T.GRGE Geonames:T.VAL Geonames:T.VALS SWEETRealm:Valley TGN:21425 TGN:21451 TGN:21452 TGN:21453 chasm coulee dale glacial gorge glacial trough gulch gully median valley shelf valley glen goe gorge graben hollow lavaka moat ravine re-entrant seachannel strath trench vale water gap Valleys are typically located between hills our mountains. valley A depression which has been formed as a result of erosion by water or ice and which is low-lying, bordered by higher ground, and especially elongate. ADL:FTT https://en.wikipedia.org/wiki/Valley chasm USGS:SDTS coulee USGS:SDTS dale USGS:SDTS glacial gorge USGS:SDTS glacial trough USGS:SDTS gulch USGS:SDTS gully Getty:TGN gully USGS:SDTS median valley ADL:FTT median valley Geonames:feature shelf valley Geonames:feature glen ADL:FTT glen USGS:SDTS goe USGS:SDTS gorge Geonames:feature gorge USGS:SDTS graben USGS:SDTS hollow ADL:FTT hollow Getty:TGN hollow USGS:SDTS moat USGS:SDTS ravine USGS:SDTS re-entrant USGS:SDTS seachannel USGS:SDTS strath USGS:SDTS trench USGS:SDTS water gap USGS:SDTS A field which is located on land and used for agricultural purposes, such as the grazing of livestock or the cultivation of crops. agricultural site field cropland grassland agricultural field A field which is located on land and used for agricultural purposes, such as the grazing of livestock or the cultivation of crops. https://en.wikipedia.org/wiki/Field_%28agriculture%29 agricultural site ADL:FTT field Geonames:feature cropland USGS:SDTS grassland USGS:SDTS A hydrographic feature characterized by the dominance of snow or ice. 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. MA:ma glacer ADL:FTT Ice NASA:earthrealm LandIce NASA:earthrealm glacial landform Getty:TGN glacier feature ADL:FTT 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. 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. https://en.wikipedia.org/wiki/Permafrost Permafrost NASA:earthrealm A landform elevated above the surrounding area. LTER:177 SWEETRealm:Elevation https://en.wikipedia.org/wiki/Elevation elevation A landform elevated above the surrounding area. MA:ma A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes. EcoLexicon:landform EcoLexicon:landforms FTT:754 FTT:96 SWEETRealm:Landform TGN:21400 TGN:21401 geological feature physiographic feature solid astronomical body part A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes. https://en.wikipedia.org/wiki/Landform geological feature ADL:FTT 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 A valley that contains, or contained, a glacier and was formed by glacial activity. Typically U-shaped in cross-section. https://en.wikipedia.org/wiki/Glacial_valley ENVO valley ENVO:00000248 envoPolar glacial valley A valley that contains, or contained, a glacier and was formed by glacial activity. Typically U-shaped in cross-section. MA:ma valley USGS:SDTS That part of the land in immediate contact with a body of water including the area between high and low water lines. coastal zone EcoLexicon:shore FTT:240 FTT:503 FTT:504 Geonames:T.SHOR SWEETRealm:Shore TGN:21481 https://en.wikipedia.org/wiki/Shore SHORE 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. USGS:SDTS coastal zone ADL:FTT SHORE USGS:SDTS shore Geonames:feature shoreface USGS:SDTS beach face USGS:SDTS foreshore USGS:SDTS inshore USGS:SDTS rivage USGS:SDTS seashore USGS:SDTS strand USGS:SDTS A landform sunken or depressed below the surrounding area. Clarify that this pertains to the planetary crust and create superclass for general topological depressions. https://github.com/EnvironmentOntology/envo/issues/486 EcoLexicon:depression FTT:175 FTT:215 FTT:216 Geonames:T.DPR Geonames:T.PAN Geonames:T.PANS SWEETRealm:Depression TGN:21454 TGN:21497 TGN:21521 barrier basin depression non tidal basin pan pan (geologic) pans tidal basin depression A landform sunken or depressed below the surrounding area. https://en.wikipedia.org/wiki/Depression_%28geology%29 barrier basin USGS:SDTS depression Geonames:feature non tidal basin USGS:SDTS pan Geonames:feature pan Getty:TGN pan (geologic) ADL:FTT pans Geonames:feature tidal basin USGS:SDTS 2 A biome is an ecosystem to which resident ecological communities have evolved adaptations. LTER:809 EcoLexicon:biome major habitat type EcosytemType There has been some concern raised (see Issue #143) about the usefulness of the assertion that organisms have evolved within a given biome. They may have evolved adaptations elsewhere and demonstrating one or the other is often not feasible. Consider relabelling to "environmental system determined by an ecological community" or similar. biome A biome is an ecosystem to which resident ecological communities have evolved adaptations. DOI:10.1186/2041-1480-4-43 https://en.wikipedia.org/wiki/Biome LTER:809 http://129.24.124.196/vocab/vocab/index.php?tema=809&/biomes major habitat type WWF:Biome EcosytemType NASA:earthrealm A biome that applies to the terrestrial realm. LTER:798 SPIRE:Terrestrial ENVO terrestrial realm ENVO:00000446 terrestrial biome A biome that applies to the terrestrial realm. https://en.wikipedia.org/wiki/Biome#Terrestrial_biomes An aquatic biome that comprises systems of open-ocean and unprotected coastal habitats, characterized by exposure to wave action, tidal fluctuation, and ocean currents as well as systems that largely resemble these. Water in the marine biome is generally within the salinity range of seawater: 30 to 38 ppt. SPIRE:Marine marine realm envoPolar marine biome An aquatic biome that comprises systems of open-ocean and unprotected coastal habitats, characterized by exposure to wave action, tidal fluctuation, and ocean currents as well as systems that largely resemble these. Water in the marine biome is generally within the salinity range of seawater: 30 to 38 ppt. ISBN-10:0618455043 MA:ma ORCID:0000-0002-4366-3088 https://en.wikipedia.org/wiki/Ocean A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids. 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. MA:ma https://en.wikipedia.org/wiki/Rock_(geology) 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. 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. https://en.wikipedia.org/wiki/Soil A significant accumulation of water which is part of a marine biome. body of marine water marine waterbody Ideas like "significant" are fuzzy and need to be modelled more accurately. The definition is a candidate for review. marine water body A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land. EcoLexicon:slope SWEETRealm:Slope https://en.wikipedia.org/wiki/Slope flank side slope A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land. MA:ma 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. 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. https://en.wikipedia.org/wiki/Air An environmental material primarily composed of dihydrogen oxide in its liquid form. 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. MA:ma 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. 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. https://en.wikipedia.org/wiki/Sediment Water which contains a significant concentration of dissolved salts. EcoLexicon:saltwater SWEETRealm:SalineWater SWEETRealm:SaltWater https://en.wikipedia.org/wiki/Saline_water salt water The threshold salt concentration for classifying water as saline varies, but typically begins at about 1,000 to 3,000 parts salt per million parts water or 0.1–0.3% salt by weight. saline water A biome which has its properties and composition determined by a water body and within which most members of resident ecological communities have adapted to life in or on water. LTER:41 aquatic biome Water which has physicochemical properties that have been determined by the processes occuring in a sea or ocean. When we have more classes representing the various processes which make seawater seawater, we can further axiomatise this class. EcoLexicon:sea_water LTER:701 SWEETRealm:SeaWater https://en.wikipedia.org/wiki/Sea_water ocean water seawater This definition refers to water that is actually in a sea or ocean. This water may have a wide range of salinity levels. sea water A material entity which determines an environmental system. 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. DOI:10.1186/2041-1480-4-43 NM:nm ORCID:0000-0002-4366-3088 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. 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. https://en.wikipedia.org/wiki/Clay A portion of enriched soil is a portion of soil with elevated levels of some material entity. ENVO ENVO:00003082 This could be demoted to an inferred class if issues with double inheritance arise. enriched soil field soil 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. 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. DOI:10.1186/2041-1480-4-43 MA:ma ORCID:0000-0002-4366-3088 URL:http://ontology.buffalo.edu/smith/articles/niches.html A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. DOI:10.1186/2041-1480-4-43 MA:ma ORCID:0000-0002-4366-3088 URL:http://ontology.buffalo.edu/smith/articles/niches.html A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings. 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. URL:http://www.merriam-webster.com/dictionary/surface Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets. EcoLexicon:aerosol SWEETRealm:Aerosol envoAtmo Should connect to PATO as "quality of an aerosol" aerosol Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets. https://en.wikipedia.org/wiki/Aerosol Silt is granular material of a size somewhere between sand and clay whose mineral origin is quartz and feldspar. 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. https://en.wikipedia.org/wiki/Silt A naturally occurring granular material composed of finely divided rock and mineral particles. 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. https://en.wikipedia.org/wiki/Sand The marine pelagic biome (pelagic meaning open sea) is that of the marine water column, from the surface to the greatest depths. ORCID:0000-0002-4366-3088 2010-03-15T11:17:06Z ENVO ENVO:01000023 envoPolar marine pelagic biome The marine pelagic biome (pelagic meaning open sea) is that of the marine water column, from the surface to the greatest depths. ISBN:0750633840 The neritic epipelagic zone biome comprises the marine water column above a continental shelf. ORCID:0000-0002-4366-3088 2010-03-15T11:19:19Z ENVO ENVO:01000032 neritic pelagic zone biome The neritic epipelagic zone biome comprises the marine water column above a continental shelf. ISBN:044482619X ISBN:0750633840 ORCID:0000-0002-4366-3088 The oceanic epipelagic zone biome comprises the marine water column offshore, beyond a continental shelf. ORCID:0000-0002-4366-3088 2010-03-15T11:19:19Z ENVO ENVO:01000033 oceanic pelagic zone biome The oceanic epipelagic zone biome comprises the marine water column offshore, beyond a continental shelf. ISBN:044482619X ISBN:0750633840 ORCID:0000-0002-4366-3088 The oceanic sea surface microlayer (SML) biome comprises the top 1000 micrometers of the marine surface waters occurring offshore, away from a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath. ORCID:0000-0002-4366-3088 2010-03-15T11:21:03Z ENVO ENVO:01000034 oceanic sea surface microlayer biome The oceanic sea surface microlayer (SML) biome comprises the top 1000 micrometers of the marine surface waters occurring offshore, away from a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath. ORCID:0000-0002-4366-3088 https://en.wikipedia.org/wiki/Sea_surface_microlayer The neritic sea surface microlayer (SML) biome comprises the top 1000 micrometers of marine surface waters occurring above a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath. ORCID:0000-0002-4366-3088 2010-03-15T11:22:09Z ENVO ENVO:01000041 neritic sea surface microlayer biome The neritic sea surface microlayer (SML) biome comprises the top 1000 micrometers of marine surface waters occurring above a continental shelf. It is the boundary layer where all exchange occurs between the atmosphere and the ocean. The chemical, physical, and biological properties of the SML differ greatly from the sub-surface water just a few centimeters beneath. ORCID:0000-0002-4366-3088 https://en.wikipedia.org/wiki/Sea_surface_microlayer A prominent or distinctive aspect, quality, or characteristic of environments occurring within the marine water column. ORCID:0000-0002-4366-3088 2010-03-16T12:10:50Z envoPolar marine pelagic feature A prominent or distinctive aspect, quality, or characteristic of environments occurring within the marine water column. ISBN-10:0618455043 ORCID:0000-0002-4366-3088 Particulate material is an environmental material which is composed of microscopic portions of solid or liquid material suspended in another environmental material. Subclasses should be assigned by inference. envoAtmo envoPolar particulate matter Environmental material derived from living organisms and composed primarily of one or more biomacromolecules. ORCID:0000-0002-4366-3088 2010-03-20T08:40:04Z EcoLexicon:organic_material biomass organic material Environmental material derived from living organisms and composed primarily of one or more biomacromolecules. ISBN-10:0618455043 ORCID:0000-0002-4366-3088 A shrubland biome is a terrestrial biome which includes, across its entire spatial extent, dense groups of shrubs. ORCID:0000-0002-4366-3088 2013-04-07T14:26:46Z Preliminary definition. shrubland biome An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system. ORCID:0000-0002-4366-3088 2013-04-07T14:35:18Z 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. environmental condition An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system. DOI:10.1186/2041-1480-4-43 A montane shrubland biome is a shrubland biome which occurs in regions elevated above sea level and which has community structure determined by elevation-dependent environmental conditions. ORCID:0000-0002-4366-3088 2013-04-07T14:40:32Z wwfBiome Preliminary definition. montane shrubland biome A system which has the disposition to environ one or more material entities. 2013-09-23T16:04:08Z 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. environmental system A system which has the disposition to environ one or more material entities. DOI:10.1186/2041-1480-4-43 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. 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 2013-10-05T12:37:41Z 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. https://en.wikipedia.org/wiki/Mineral Water vapour is a vapour which is the gas phase of water. ORCID:0000-0002-4366-3088 2013-10-10T07:58:18Z aqueous vapor aqueous vapour water vapor 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. https://en.wikipedia.org/wiki/Water_vapor aqueous vapor https://en.wikipedia.org/wiki/Water_vapor aqueous vapour https://en.wikipedia.org/wiki/Water_vapor water vapor https://en.wikipedia.org/wiki/Water_vapor 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 2013-10-10T08:14:50Z 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. https://en.wikipedia.org/wiki/Atmosphere https://en.wikipedia.org/wiki/Physical_geography Atmospheric water vapour is water vapour that is part of an atmosphere. ORCID:0000-0002-4366-3088 2013-10-10T08:22:07Z atmospheric water vapor ENVO ENVO:01000268 envoPolar atmospheric water vapour Atmospheric water vapour is water vapour that is part of an atmosphere. https://en.wikipedia.org/wiki/Water_vapor atmospheric water vapor https://en.wikipedia.org/wiki/Water_vapor A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions. ORCID:0000-0002-4366-3088 2013-10-12T17:21:09Z 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. DOI:10.1641/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2 URL:http://worldwildlife.org/biomes 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. ORCID:0000-0002-4366-3088 2013-10-13T12:01:28Z 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. https://en.wikipedia.org/wiki/Ice ice http://www.eionet.europa.eu/gemet/concept/4131 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. ORCID:0000-0002-4366-3088 2013-10-13T18:32:46Z 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. https://en.wikipedia.org/wiki/ecozone A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface. ORCID:0000-0002-4366-3088 2013-10-15T16:42:02Z envoPolar Preliminary definition. layer A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface. Wiktionary:layer A layer which is part of a lake. ORCID:0000-0002-4366-3088 2013-10-15T16:57:43Z ENVO ENVO:01000283 envoPolar Note that this class does not contain metalimnion as a subclass. The metaliminon is classified as a thermocline. lake layer A mass of ice. Class should be populated by inference and asserted subclasses redistributed. ORCID:0000-0002-4366-3088 2013-10-15T19:49:11Z envoPolar ice mass A layer that is part of a marine water body. ORCID:0000-0002-4366-3088 envoMarine envoPolar marine layer A layer that is part of a marine water body. ORCID:0000-0002-4366-3088 An endolithic environment is an environment that exists within solid rock. endolithic environment An environmental system which has its properties and dynamics determined by saline water. Water (saline) envoEmpo envoOmics envoPolar saline water environment Water (saline) http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An environment which has a lower temperature than some local or global average. 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 anthropogenic environment is an environmental system which is the product of human activity. Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic. anthropogenic environment A high osmolarity environment is an environment in which entities are exposed to high concentrations of solutes. high osmolarity environment An environment whose dynamics are strongly influenced by water. aquatic environment A rocky slope is a slope which has a surface primarily composed of rock. rocky slope A marine environment and enviroment which is determined by a marine water body. envoPolar marine environment A marine environment and enviroment which is determined by a marine water body. NM:nm An environmental system determined by seawater. ocean water environment envoPolar sea water environment A planetary surface is a surface layer where the solid or liquid material of a planet comes into contact with an atmosphere or outer space. a useful class: this can be used to define sub-terrestrial and sub-marine entities planetary surface A layer in a water mass, itself composed primarily of water. envoPolar This class will eventually be populated by inference, and its asserted subclasses removed. aquatic layer A montane condition is an environmental condition in which an altitude range falls between mid-altitude forests and the tree line. ORCID:0000-0002-4366-3088 LTER:350 envoPolar The exact level of the tree line varies with local climate, but typically the tree line is found where mean monthly soil temperatures never exceed 10.0 degrees C and the mean annual soil temperatures are around 6.7 degrees C. In the tropics, this region is typified by montane rain forest (above 3,000 ft) while at higher latitudes coniferous forests often dominate. montane A montane condition is an environmental condition in which an altitude range falls between mid-altitude forests and the tree line. https://en.wikipedia.org/wiki/Altitudinal_zonation The exact level of the tree line varies with local climate, but typically the tree line is found where mean monthly soil temperatures never exceed 10.0 degrees C and the mean annual soil temperatures are around 6.7 degrees C. In the tropics, this region is typified by montane rain forest (above 3,000 ft) while at higher latitudes coniferous forests often dominate. https://en.wikipedia.org/wiki/Altitudinal_zonation An altitudinal condition is an environmental condition in which ranges of factors such as temperature, humidity, soil composition, solar irradiation, and tree density vary with ranges in altitude. ORCID:0000-0002-4366-3088 envoPolar Depending on the latitude (and, to a lesser extent, other factors), the actual location of the zones where these conditions are in effect will change. altitudinal condition An altitudinal condition is an environmental condition in which ranges of factors such as temperature, humidity, soil composition, solar irradiation, and tree density vary with ranges in altitude. https://en.wikipedia.org/wiki/Altitudinal_zonation An unbroken expanse (as of ice) field An unbroken expanse (as of ice) http://www.merriam-webster.com/dictionary/field A layer which is determined by a form of vegetation. forest layer forest stratum woodland layer woodland stratum Usually found in woodlands and forests. vegetation layer Snow is an environmental material which is primarily composed of flakes of crystalline water ice. envoPolar snow Snow is an environmental material which is primarily composed of flakes of crystalline water ice. http://www.eionet.europa.eu/gemet/concept/7769 https://en.wikipedia.org/wiki/Snow 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. 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 lentic water body is a water body in which the accumulated water, in its totality, has very little to no directed flow. lentic water body Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase. 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. https://en.wikipedia.org/wiki/Condensation Land is a planetary surface that is not covered by liquid. ground Land may more properly be represented as part of a planetary surface rather than a sublcass. land Land is a planetary surface that is not covered by liquid. Adpated from https://en.wikipedia.org/wiki/Planetary_surface Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies. space envoAstro outer space Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies. https://en.wikipedia.org/wiki/Outer_space A planetary crust is the outermost solid shell of a rocky planet or natural satellite, which is chemically distinct from the underlying mantle. crust This class is meant to be applicable accross planets. Earth's crust would be an instance. planetary crust A planetary crust is the outermost solid shell of a rocky planet or natural satellite, which is chemically distinct from the underlying mantle. https://en.wikipedia.org/wiki/Crust_(geology) A planetary structural layer is laminar part of a terrestrial planet or other rocky body large enough to have differentiation by density. Planetary layers have differing physicochemical properties and composition. Label should be improved to match definition. planetary structural layer A mass of water. water mass A coast is the area where land meets the sea, ocean, or lake. 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. https://en.wikipedia.org/wiki/Coast Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity. 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. https://en.wikipedia.org/wiki/Precipitation Condensation is a process during which a gas undergoes a phase transition into a liquid. condensation process Condensation is a process during which a gas undergoes a phase transition into a liquid. https://en.wikipedia.org/wiki/Condensation An environmental system which can sustain and allow the growth of an ecological population. 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:EnvO A part of an astronomical body which is primarily composed of a continuous volume of gaseous or aerosolised material held in shape by one or more environmental processes. This may not need to be in the atmosphere, also note that "meteor" will do much of the same work. envoAtmo Similar, in spirit, to landform. This class may need to be split into aerosols and 'pure' volumes of gas. aeroform A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely. 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. http://www.merriam-webster.com/dictionary/gas An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space. celestial body envoAstro Astronomical bodies are usually cohesive, thus the use of the term 'object' sensu BFO 'object'. astronomical body An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space. https://en.wikipedia.org/wiki/Astronomical_object A planet is an astronomical body orbiting a star or stellar remnant that is massive enough to be rounded by its own gravity, is not massive enough to cause thermonuclear fusion, and has cleared its neighbouring region of planetesimals. envoAstro envoPolar Considerable debate on the definition of planet exists. planet A planet is an astronomical body orbiting a star or stellar remnant that is massive enough to be rounded by its own gravity, is not massive enough to cause thermonuclear fusion, and has cleared its neighbouring region of planetesimals. http://solarsystem.nasa.gov/planets/whatisaplanet https://en.wikipedia.org/wiki/Planet 1 An object which is composed of one or more gravitationally bound structures that are associated with a position in space. celestial object envoAstro If there is only one astronomical body involved, this class is equivalent to ENVO:01000799. This may be problematic with reasoning, but it seems to be true to the rather fuzzy definitions found thus far. astronomical object An object which is composed of one or more gravitationally bound structures that are associated with a position in space. https://en.wikipedia.org/wiki/Astronomical_object A material part of an astronomical body. envoAstro envoPolar astronomical body part An environmental material which is in a solid state. This is a defined class: its subclasses will not be asserted, but filled by inference. solid environmental material An environmental material which is in a liquid state. envoPolar This is a defined class: its subclasses will not be asserted, but filled by inference. liquid environmental material 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. 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. http://www.biology-online.org/dictionary/Biosphere https://en.wikipedia.org/wiki/Biosphere 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. http://www.biology-online.org/dictionary/Biosphere https://en.wikipedia.org/wiki/Biosphere A cryosphere is that part of a planet which is primarily composed of water is in solid form. 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. https://en.wikipedia.org/wiki/Cryosphere An astronomical body part which is composed of the combined mass of water found on, under, and over the surface of a planet. envoAstro envoPolar This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class. hydrosphere An astronomical body part which is composed of the combined mass of water found on, under, and over the surface of a planet. https://en.wikipedia.org/wiki/Hydrosphere 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. 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. https://en.wikipedia.org/wiki/Precipitation_%28chemistry%29 https://en.wikipedia.org/wiki/Precipitation A hydrological process in which irregular aggregates of snow fall to a planetary surface. snow fall environmental_hazards envoPolar snowfall 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. non-anthropised environment non-anthropized environment 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 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. https://en.wikipedia.org/wiki/Anthropization https://en.wikipedia.org/wiki/Natural_environment A process during which a natural environmental system is altered by human action. 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. https://en.wikipedia.org/wiki/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. https://en.wikipedia.org/wiki/Anthropization A planet that is composed primarily of silicate rocks or metals. rocky planet telluric planet Earth-like planet envoAstro terrestrial planet A planet that is composed primarily of silicate rocks or metals. https://en.wikipedia.org/wiki/Terrestrial_planet A process whereby a volume of liquid moves due to a disequilibrium of physical forces. 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. https://en.wikipedia.org/wiki/Wind A process during which a volume of water is transported due to a disequilibria in physical forces. environmental_hazards water flow process An environmental system which is determined by materials bearing roughly homogeneous qualities. Organisational class. Not intended for annotation. environmental system determined by a quality An environmental system within which an environmental material strongly influences the system's composition and properties. 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 An environmental system which is determined by a living organism. host-associated environment envoEmpo envoOmics environmental system determined by an organism An environmental system determined by a green plant. Plant plant environment Viridiplantae-associated environment envoEmpo envoOmics plant-associated environment Plant http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An environmental system determined by an animal. Animal animal environment Metazoan-associated environment envoEmpo envoMeo envoOmics animal-associated environment Animal http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ A meteor is any matter- or energy-based entity which is located in the atmosphere of an astronomical body. envoAtmo meteor A meteor is any matter- or energy-based entity which is located in the atmosphere of an astronomical body. https://cloudatlas.wmo.int/other-meteors.html A meteor which is primarily composed of water. envoAtmo hydrometeor A meteor which is primarily composed of water. https://cloudatlas.wmo.int/other-meteors.html A meteor which is primarily composed of rock. envoAtmo lithometeor A lake which has formed as the result of processes that are not or are only minimally driven by human activity. This class is to be filled by inference. natural lake A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium. 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. https://en.wikipedia.org/wiki/Radiation An environment which is determined by materials which bear significant concentrations of salts. Saline 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 Saline http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An environmental system which has its properties and dynamics determined by soil. Soil (non-saline) envoEmpo envoOmics soil environment Soil (non-saline) http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An environmental system which has its properties and dynamics determined by sediment. envoEmpo envoOmics sediment environment An environmental system which has its properties and dynamics determined by an aerosol. Aerosol (saline) envoEmpo envoOmics aerosol environment Aerosol (saline) http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An environmental system which has its properties and dynamics determined by a saline aerosol. Aerosol (saline) envoEmpo envoOmics saline aerosol environment Aerosol (saline) http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ seaspray or other aerosolized saline material (>5 psu) An environmental system which has its properties and dynamics determined by an aerosol with a low concentration of dissolved solutes. Aerosol (non-saline) envoEmpo envoOmics non-saline aerosol environment Aerosol (non-saline) http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ aerosolized dust or liquid An environmental system determined by part of a living or dead animal, or a whole small animal. environment associated with an animal part or small animal An environmental system determined by part of a living or dead plant, or a whole small plant. Plant corpus envoEmpo envoMeo envoOmics environment associated with a plant part or small plant Plant corpus http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/ An astronomical body which is composed of rocky or metallic materials and is considerably smaller than asteroids. envoAstro meteoroid An astronomical body which is composed of rocky or metallic materials and is considerably smaller than asteroids. https://en.wikipedia.org/wiki/Meteoroid A material which is composed primarily of one or more pure metals and which shows their properties. 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. https://en.wikipedia.org/wiki/Metal An aerosol which has non-gaseous parts that are primarily composed of liquid droplets. SWEETRealm:Aerosol liquid aerosol envoAtmo aerosolised liquids An aerosol which has non-gaseous parts that are primarily composed of liquid droplets. https://en.wikipedia.org/wiki/Aerosol An aerosol which has non-gaseous parts that are primarily composed of solid particles. SWEETRealm:Aerosol solid aerosol envoAtmo aerosolised solids An aerosol which has non-gaseous parts that are primarily composed of solid particles. https://en.wikipedia.org/wiki/Aerosol An environmental system which includes both living and non-living components. 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. https://en.wikipedia.org/wiki/Ecosystem LTER:173 http://129.24.124.196/vocab/vocab/index.php?tema=173&/ecosystems A planet which is primarily composed of hydrogen and helium. envoAstro Gas giants are composed of about 90% hydrogen and helium. Jupiter and Saturn are examples of gas giants. gas planet A planet which is primarily composed of hydrogen and helium. http://solarsystem.nasa.gov/planets/whatisaplanet https://en.wikipedia.org/wiki/List_of_planet_types https://en.wikipedia.org/wiki/Planet An ice is an environmental material which is either frozen or which is maintained in a solid state by gravitational forces or pressure. 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 A planet which has a surface layer that nearly completely or completely covered by water, and which has a substantial portion of its mass composed of water. An axiom to express that the planet has a 'substantial' proportion of its mass in the form of water wound enhance this class. aquaplanet panthalassic planet water world envoAstro While this planetary form is still mostly theoretical, strong candidates exist such as the extrasolar planet GJ 1214 b and ocean planet candidate Kepler-22b. ocean planet A planet which has a surface layer that nearly completely or completely covered by water, and which has a substantial portion of its mass composed of water. https://en.wikipedia.org/wiki/Ocean_planet A planet which has a surface layer that nearly completely or completely covered by ice, and which has a substantial portion of its mass composed of ice. cryoplanet envoAstro While this planetary form is still mostly theoretical, strong candidates exist such as OGLE-2005-BLG-390Lb, OGLE-2013-BLG-0341L b and MOA-2007-BLG-192Lb. Pluto was considered an ice planet until its reclassification in 2006 CE. Surface temperatures of ice planets would have to be below 260 K (−13°C) if composed primarily of water, below 180 K (−93°C) if primarily composed of CO2 and ammonia, and below 80 K (−193°C) if composed primarily of methane. ice planet A planet which has a surface layer that nearly completely or completely covered by ice, and which has a substantial portion of its mass composed of ice. https://en.wikipedia.org/wiki/Ice_planet While this planetary form is still mostly theoretical, strong candidates exist such as OGLE-2005-BLG-390Lb, OGLE-2013-BLG-0341L b and MOA-2007-BLG-192Lb. Pluto was considered an ice planet until its reclassification in 2006 CE. Surface temperatures of ice planets would have to be below 260 K (−13°C) if composed primarily of water, below 180 K (−93°C) if primarily composed of CO2 and ammonia, and below 80 K (−193°C) if composed primarily of methane. https://en.wikipedia.org/wiki/Ice_planet A gas planet which has an atmosphere composed primarily of helium. The placement of this class assumes that some traces of hydrogen are left in the atmosphere. If this is not the case, the axiom on gas planet must be updated. envoAstro A helium planet might form via hydrogen evaporation from a gaseous planet orbiting close to a star. Low-mass white dwarfs may transition into objects which are essentially helium planets by hydrogen depletion through mass transfer to a massive object such as a neutron star. Gliese 436 b is a candidate helium planet. helium planet A gas planet which has an atmosphere composed primarily of helium. https://en.wikipedia.org/wiki/Helium_planet A helium planet might form via hydrogen evaporation from a gaseous planet orbiting close to a star. Low-mass white dwarfs may transition into objects which are essentially helium planets by hydrogen depletion through mass transfer to a massive object such as a neutron star. Gliese 436 b is a candidate helium planet. https://en.wikipedia.org/wiki/Helium_planet A material which is composed primarily of chemical elements and compounds with relatively low boiling points, equilibrium condensation temperatures below 1300 Kelvin, and which are part of the crust or atmosphere of a moon or planet. Add and axiomatise with moon and lunar crust volatile envoAstro Examples include nitrogen, water, carbon dioxide, ammonia, hydrogen, methane and sulfur dioxide. In astrogeology, these compounds, in their solid state, often comprise large proportions of the crusts of moons and dwarf planets. volatile astrogeological material A material which is composed primarily of chemical elements and compounds with relatively low boiling points, equilibrium condensation temperatures below 1300 Kelvin, and which are part of the crust or atmosphere of a moon or planet. https://en.wikipedia.org/wiki/Volatiles Examples include nitrogen, water, carbon dioxide, ammonia, hydrogen, methane and sulfur dioxide. In astrogeology, these compounds, in their solid state, often comprise large proportions of the crusts of moons and dwarf planets. https://en.wikipedia.org/wiki/Volatiles An astrogeological volatile which is composed primarily of chemical compounds with boiling points around those of hydrogen and helium. gas envoAstro This is a term native to the fields of planetary science and astrophysics. Hydrogen has a boiling point of 20.271 Kelvin and a melting point of 13.99 Kelvin. Helium has a boiling point of 4.222 Kelvin and a melting point of 0.95 Kelvin. astrogeological gas An astrogeological volatile which is composed primarily of chemical compounds with boiling points around those of hydrogen and helium. https://en.wikipedia.org/wiki/Volatiles A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms. Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities. geodiversity A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms. https://en.wikipedia.org/wiki/Geodiversity Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities. 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 envoMeo envoOmics environment associated with an aquatic invertebrate http://purl.jp/bio/11/meo/MEO_0000871 Not currently live, may need to be switched to alternative PURLs. The surface layer of a volume of water. 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 mass of sediment. surface of a sedimentary mass surface sediment sediment surface An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it. terrestrial environmental zone An environmental zone which is bounded by material parts of a marine environment. 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 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. 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 Wetland EstuarineWetland LacustrineWetland MarineWetland PalustrineWetland RiparianWetland TerrestialWetland 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. https://en.wikipedia.org/wiki/Wetland WETLAND USGS:SDTS Wetland NASA:earthrealm EstuarineWetland NASA:earthrealm LacustrineWetland NASA:earthrealm MarineWetland NASA:earthrealm PalustrineWetland NASA:earthrealm RiparianWetland NASA:earthrealm TerrestialWetland 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 A natural environment which is located on a land mass. terrestrial natural environment A natural environment which is within a water body. aquatic natural environment A layer which is primarily composed of some liquid material. liquid layer A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid. 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. water ice layer An environmental zone which is part of an atmosphere. atmospheric area atmospheric zone A vegetated area is a geographic feature which has ground cover dominated by plant communities. ORCID:0000-0002-4366-3088 envoPolar vegetated area A geographic feature which is primarily composed of a continuous volume of liquid water held in shape or sustained by an environmental process. Should create links to envrionmental process with new relation like "sustained_by" Similar, in spirit, to landform. hydroform Should create links to envrionmental process with new relation like "sustained_by" ORCID:0000-0002-4366-3088 A liquid surface layer which is in contact with air. liquid air-water interface layer A liquid surface layer which is in contact with air. liquid surface layer A surface layer which is composed primarily of solid environmental material. solid surface layer A body of water which is primarily composed of saline water. saline body of water This class has its subclasses populated by inference. saline water body 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. 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. https://en.wikipedia.org/wiki/Advection https://en.wikipedia.org/wiki/Intensive_and_extensive_properties 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. 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. https://en.wikipedia.org/wiki/Erosion A material transport process during which solid or liquid particles are directly introduced into a volume of gas. primary aerosol formation primary aerosol formation process A material transport process during which solid or liquid particles are directly introduced into a volume of gas. https://en.wikipedia.org/wiki/Aerosol https://en.wikipedia.org/wiki/Particulates A process during which an ecosystem - natural or anthropised - is changed by the actions of humans. http://orcid.org/0000-0002-4366-3088 anthropogenic ecosystem conversion process http://orcid.org/0000-0002-4366-3088 body of liquid A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes. http://orcid.org/0000-0002-4366-3088 liquid astronomical body part A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes. https://en.wikipedia.org/wiki/Landform A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes. http://orcid.org/0000-0002-4366-3088 gaseous astronomical body part A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes. https://en.wikipedia.org/wiki/Landform A part of an astronomical body which is primarily composed of a continuous volume of liquid or gaseous material, shaped by one or more environmental processes. http://orcid.org/0000-0002-4366-3088 2018-10-04T13:59:22Z fluid astronomical body part A part of an astronomical body which is primarily composed of a continuous volume of liquid or gaseous material, shaped by one or more environmental processes. https://en.wikipedia.org/wiki/Landform A surface layer where the solid or liquid material of an astronomical body comes into contact with an atmosphere or outer space. http://orcid.org/0000-0002-4366-3088 2018-10-04T16:55:57Z a useful class: this can be used to define sub-terrestrial and sub-marine entities surface of an astronomical body A material transformation process during which a material's viscosity increase either through a reduction in temperature or through chemical reactions. http://orcid.org/0000-0002-4366-3088 2019-01-14T18:47:32Z 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. https://en.wikipedia.org/wiki/Congelation Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question. https://en.wikipedia.org/wiki/Congelation Land which is below the freezing point of water. http://orcid.org/0000-0002-4366-3088 2019-01-14T21:18:19Z http://sweetontology.net/realmCryo/FrozenGround frozen ground Perennially and seasonally frozen ground can vary from being partially to extensively frozen depending on the extent of the phase change. It may be described as hard frozen ground, plastic frozen ground, or dry frozen ground, depending on the pore ice and unfrozen water contents and its compressibility under load. frozen land Land which is below the freezing point of water. https://orcid.org/0000-0003-4808-4736 Perennially and seasonally frozen ground can vary from being partially to extensively frozen depending on the extent of the phase change. It may be described as hard frozen ground, plastic frozen ground, or dry frozen ground, depending on the pore ice and unfrozen water contents and its compressibility under load. https://orcid.org/0000-0003-4808-4736 Soil which is below the freezing point of water. http://orcid.org/0000-0002-4366-3088 2019-01-14T21:26:59Z frozen soil A water surface that is part of a water body. http://orcid.org/0000-0002-4366-3088 2019-02-27T21:22:13Z surface layer of a water body An ecoregion which is located on a landmass. http://orcid.org/0000-0002-4366-3088 2019-03-05T17:40:44Z https://www.worldwildlife.org/biome-categories/terrestrial-ecoregions terrestrial ecoregion A surface layer of a water body which is part of an ocean or sea. http://orcid.org/0000-0002-4366-3088 2019-03-06T01:22:01Z 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 process in which includes the components of an environmental system as participants. This is a convenience class for organisation and should not be used for annotation. environmental system process A process which occurs within an atmosphere. This class will be populated by inference and is primarily organisational. atmospheric process A process during which humans apply technology to alter the magnitude, duration, rate, or impact of an environmental process. anthropogenic modulatory intervention process An environmental process which is driven by the action of humans. anthropogenic environmental process An action of exogenic processes (such as water flow or wind) which remove environmental material from one part of a planet's crust, transporting it to another location where it is deposited. envoPolar planetary erosion An action of exogenic processes (such as water flow or wind) which remove environmental material from one part of a planet's crust, transporting it to another location where it is deposited. https://en.wikipedia.org/wiki/Erosion An environmental process which has water - in any of its states - as a participant. This classes asserted subclasses will be moved away as it should be an inferred class. hydrological process A process during which the mass of one or more materials, present within a given site, increases. 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 material is displaced from its original location and transported either to a new location or back to the original location. 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 depression which is part of a planetary crust, is of geographic scale, and is partially or completely enclosed. The general semantics of depression and geographic basin are still to be worked out see https://github.com/EnvironmentOntology/envo/issues/486 http://orcid.org/0000-0002-3410-4655 http://orcid.org/0000-0002-4366-3088 envoPolar geographic basin A depression which is part of a planetary crust, is of geographic scale, and is partially or completely enclosed. https://en.wikipedia.org/wiki/Basin Sediment which has been transported through the marine water column, settling on the seafloor. 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. https://en.wikipedia.org/wiki/Pelagic_sediment#_note-8 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. http://orcid.org/0000-0002-3410-4655 http://orcid.org/0000-0002-4366-3088 envoPolar sedimentation in a water body A process during which a portion of some environmental material is converted into a different material or a collection of materials. 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 geographic feature which is primarily composed of a continuous mass of snow and/or ice. Place holder class. Also the axiom should be changed to something along the lines of 'primairly composed of’ some ‘environmental material’ and ‘has quality’ frozen once PATO:frozen is imported. http://orcid.org/0000-0002-3410-4655 http://orcid.org/0000-0002-4366-3088 envoPolar cryoform A mass of snow. http://orcid.org/0000-0002-3410-4655 http://orcid.org/0000-0002-4366-3088 envoPolar snow mass The temperature of some environmental material. environmental material temperature temperature of environmental material The temperature of some air. air temperature temperature of air The porosity of some soil. soil porosity porosity of soil The composition of some soil. soil composition composition of soil The structure of some soil. soil structure structure of soil The temperature of some soil. soil temperature temperature of soil The wetness of some soil. soil wetness wetness of soil The temperature of some water. water temperature temperature of water The composition of some water. water composition composition of water The concentration of a oxygen when measured in water. water oxygen concentration concentration of oxygen in water An environment which is determined by an anatomical entity. anatomical entity environment The concentration of dioxygen when measured in water. water dioxygen concentration concentration of dioxygen in water A substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure. Damion Dooley https://en.wikipedia.org/wiki/Food food product The FoodOn product type class is provided as a food product category tree under which new food product categories and food products themselves can be placed. This tree has upper level categories inspired from other product type schemes like the US Code of Federal Regulations. However it has a much greater depth to it than the other product type schemes in an effort to group related products together. The basis of this tree was inherited from the environment ontology (ENVO). foodon product type This food product type includes food products which are derived from or produced by a plant. plant food product A food product which is derived from or produced by an animal that has a vertibrae. Damion Dooley vertebrate animal food product invertebrate animal food product food component food component product food product by organism food food material Invertebrates are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. animal invertebrate animal food object quality A multicellular eukaryotic heterotrophic organism within the kingdom Animalia. animal A food product not including meat and animal tissue products (such as gelatin or animal-derived rennet). https://en.wikipedia.org/wiki/Vegetarian_cuisine 2019-09-11T21:12:43Z vegetarian food vegetarian food product A food product type is a class of food products that is differentiated by its food composition, processing and/or consumption characteristics. This does not include brand name products but it may include generic food dish categories. Damion Dooley http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0361 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. food product type http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1041 LanguaL curation note: A chemical food component is a food substance derived from a nonliving source (e.g., salt, water or synthesized compounds). chemical food component chemical food product Mammals (from Latin mamma "breast") are vertebrate animals constituting the class Mammalia, and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones. mammal A vertebrate animal is any species of organism within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,276 species described. animal vertebrate animal http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1564 This was LanguaL definition: Individual plant or animal from which the food product or its major ingredient is derived; also a chemical food source [FDA CFSAN 1995]. food source This section and its narrover terms refer to the European Commission food additive regulation according to COMMISSION REGULATION (EU) No 1129/2011 of 11 November 2011 amending Annex II to Regulation (EC) No 1333/2008 of the European Parliament and of the Council by establishing a Union list of food additives [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2011:295:0001:0177:EN:PDF] and its basis, the four Food Additive Directives: the EEC Framework Directive on Food Additives (89/107/EEC), the Directive on colours (94/36/EC), the Directive on sweeteners (94/35/EC) and the 'miscellaneous' Directive (95/2/EC) plus amendments [http://ec.europa.eu/food/fs/sfp/flav_index_en.html] and/or Codex Alimentarius Commission General Standard for Food Additives (CODEX STAN 192, revised 2011) [http://www.codexalimentarius.net/download/standards/4/CXS_192e.pdf]. If used for food supplement substances, thissection and its narrover terms refer to the European Commission regulation in general [http://ec.europa.eu/food/food/labellingnutrition/supplements/index_en.htm] and specifically to the EC Directive on the approximation of the laws of the Members States relating to food supplements (2002/46/EC) [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2002:183:0051:0057:EN:PDF]. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B2972 Damion Dooley's note: manysubclasses here are currently originating from LanguaL additives that have not yet been matched to CHEBI ontology terms. If matches are possible they will be implemented over time, at which point the corresponding FoodOn id's will be deprecated. food additive A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. molecular process molecular function molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. GOC:pdt catalytic activity receptor activity Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. receptor binding receptor ligand receptor-associated protein activity signaling receptor binding Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. GOC:bf GOC:ceb ISBN:0198506732 The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. ligand binding The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. GOC:ceb GOC:mah ISBN:0198506732 Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). protein amino acid binding glycoprotein binding protein binding Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). GOC:go_curators Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. cell communication Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:mah The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. signaling cascade signalling cascade signaling pathway signalling pathway signal transduction The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GOC:go_curators GOC:mtg_signaling_feb11 signalling pathway GOC:mah A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. 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. janelomax 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt 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. GOC:go_curators GOC:isa_complete Any process that modulates the frequency, rate or extent of signal transduction. regulation of signaling pathway regulation of signalling pathway regulation of signal transduction Any process that modulates the frequency, rate or extent of signal transduction. GOC:sm regulation of signalling pathway GOC:mah Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. cell physiology cellular physiological process cell growth and/or maintenance single-organism cellular process cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. regulation of cell communication Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb true kinase activity transferase activity transferase activity, transferring phosphorus-containing groups Any process that modulates the frequency, rate or extent of a signaling process. regulation of signaling process regulation of signalling process regulation of signaling Any process that modulates the frequency, rate or extent of a signaling process. GOC:mtg_signal regulation of signaling process GOC:bf regulation of signalling process GOC:mah The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. biological signaling signaling process signalling signalling process single organism signaling signaling The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. GOC:mtg_signal GOC:mtg_signaling_feb11 GOC:signaling signalling process GOC:mah The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed. receptor regulator activity The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed. GOC:ceb The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased. receptor activator activity signaling receptor activator activity The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased. GOC:ceb Any process that modulates the frequency, rate or extent of protein binding. regulation of protein binding Any process that modulates the frequency, rate or extent of protein binding. GOC:go_curators The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands). receptor agonist activity signaling molecule signaling receptor ligand activity vitamin D receptor activator activity receptor ligand activity The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands). GOC:kv GOC:molecular_function_refactoring GOC:pdt receptor agonist activity GOC:molecular_function_refactoring Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. regulation of response to stimulus Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. regulation of physiological process regulation of biological process Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:ai GOC:go_curators Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. regulation of cellular physiological process regulation of cellular process Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. physiological response to stimulus response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GOC:ai GOC:bf Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. regulation of binding Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. cellular response to stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. GOC:bf GOC:jl Any process that modulates a measurable attribute of any biological process, quality or function. regulation biological regulation Any process that modulates a measurable attribute of any biological process, quality or function. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. regulation of a molecular function regulation of molecular function Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GOC:isa_complete A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators. molecular function regulator A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators. GOC:dos GOC:pt Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor. regulation of receptor ligand regulation of receptor binding Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor. GOC:TermGenie GOC:signaling regulation of receptor ligand GOC:TermGenie A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. measurement unit label a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. experiment objective objective specification a directive information entity that describes an action the bearer will take action specification A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label datum label Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. software A quality of an information bearer that imparts the information content information carrier data item Data items include counts of things, analyte concentrations, and statistical summaries. 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. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. directive information entity A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. dot plot A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. graph A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. algorithm 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) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file data format specification data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. image 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 A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. plan specification A material entity in which a concretization of an information content entity inheres. material information bearer A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. histogram A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. heatmap A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. dendrogram A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. scatter plot 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 An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. figure A figure that expresses one or more propositions diagram A collection of information content entities intended to be understood together as a whole document 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. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls centrally registered identifier PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls centrally registered identifier registry GC_ID:1 ncbi_taxonomy all NCBITaxon:1 root all all Vira Viridae viruses Viruses Vira Viridae viruses Teleostomi bony vertebrates Euteleostomi bony vertebrates GC_ID:1 ncbi_taxonomy biota NCBITaxon:131567 cellular organisms biota biota Dipnotetrapodomorpha Boreotheria Boreoeutheria Boreotheria 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 Homo/Pan/Gorilla group Homininae Homo/Pan/Gorilla group Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes Archaea Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes GC_ID:1 PMID:23020233 PMID:30257078 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes NCBITaxon:2759 Eukaryota eucaryotes eucaryotes eukaryotes eukaryotes Eucarya Eucarya Eucaryotae Eucaryotae Eukarya Eukarya Eukaryotae Eukaryotae eukaryotes eukaryotes Euarchontoglires Anthropoidea Simiiformes Anthropoidea ape apes Hominoidea ape apes tetrapods Tetrapoda tetrapods amniotes Amniota amniotes Theria Theria <Mammalia> Theria <mammals> Theria Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants Chlorobionta Chlorophyta/Embryophyta group Chloroplastida chlorophyte/embryophyte group green plants Viridiplantae Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants green plants Chlorobionta Chlorobionta Chlorophyta/Embryophyta group Chlorophyta/Embryophyta group Chloroplastida chlorophyte/embryophyte group chlorophyte/embryophyte group green plants green plants GC_ID:1 ncbi_taxonomy Fungi/Metazoa group opisthokonts NCBITaxon:33154 Opisthokonta Fungi/Metazoa group Fungi/Metazoa group opisthokonts opisthokonts metazoans multicellular animals Animalia animals Metazoa metazoans multicellular animals Animalia animals Bilateria deuterostomes Deuterostomia deuterostomes Haplorrhini mammals mammals Mammalia mammals mammals Eumetazoa chordates chordates Chordata chordates chordates Vertebrata vertebrates vertebrates Vertebrata <Metazoa> Vertebrata <vertebrates> Vertebrata vertebrates vertebrates Gnathostomata jawed vertebrates Gnathostomata <vertebrate> Gnathostomata <vertebrates> Gnathostomata jawed vertebrates Sarcopterygii Craniata Craniata <chordata> Craniata <chordates> Craniata eutherian mammals placental mammals placentals Placentalia placentals Eutheria eutherian mammals placental mammals placentals Placentalia placentals primate Primata primates Primates primate Primata primates Catarrhini great apes Pongidae Hominidae great apes Pongidae humans Homo humans human man humans Homo sapiens human man A processual entity that realizes a plan which is the concretization of a plan specification. planned process a regulatory role involved with making and/or enforcing relevant legislation and governmental orders regulator role a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. regulatory role a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. material supplier role A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. classified data set Is a material entity that is created or changed during material processing. processed material A planned process which results in physical changes in a specified input material material processing a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation specimen role An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. organization A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. protocol A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. regulatory agency an objective specifiction that creates an specific output object from input materials. material transformation objective Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process manufacturing is the objective to manufacture a material of a certain function (device) manufacturing objective a planned process that carries out a study design study design execution Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. manufacturer role A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. clustered data set A planned process with the objective of collecting a specimen. specimen collection process A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. class prediction data transformation A objective specification to obtain a material entity for potential use as an input during an investigation. specimen collection objective A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. support vector machine A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. decision tree induction objective A decision tree building data transformation is a data transformation that has objective decision tree induction. decision tree building data transformation a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. GenePattern software Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold peak matching A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. k-nearest neighbors A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. CART A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. statistical model validation A person or organization that has a manufacturer role manufacturer is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person service provider role A specimen that has been intentionally physically modified. processed specimen A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. categorical label A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. questionnaire A value specification that is specifies one category out of a fixed number of nominal categories categorical value specification An information content entity that specifies a value within a classification scheme or on a quantitative scale. value specification A material entity that has two or more specimens as its parts. collection of specimens A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. histologic grade according to AJCC 7th edition A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. histologic grade according to the Fuhrman Nuclear Grading System A categorical value specification that is a histologic grade assigned to a ovarian tumor. histologic grade for ovarian tumor A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. histologic grade for ovarian tumor according to a two-tier grading system A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). histologic grade for ovarian tumor according to the World Health Organization A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. pathologic primary tumor stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. pathologic primary tumor stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. pathologic primary tumor stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. pathologic primary tumor stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. pathologic lymph node stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. pathologic lymph node stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. pathologic lymph node stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. pathologic lymph node stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. pathologic distant metastases stage for colon according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. pathologic distant metastases stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. pathologic distant metastases stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. pathologic distant metastases stage for ovary according to AJCC 7th edition A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. clinical tumor stage group according to AJCC 7th edition A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. International Federation of Gynecology and Obstetrics cervical cancer stage value specification A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. International Federation of Gynecology and Obstetrics ovarian cancer stage value specification A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). performance status value specification A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. Eastern Cooperative Oncology Group score value specification A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. Karnofsky score vaue specification organism animal fungus plant virus 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. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism A material entity that has the specimen role. specimen A planned process that produces output data from input data. data transformation is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data leave one out cross validation method A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). k-means clustering A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). hierarchical clustering A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. dimensionality reduction A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. principal components analysis dimensionality reduction An planned process that creates images, diagrams or animations from the input data. data visualization An objective specification to transformation input data into output data data transformation objective A partitioning data transformation is a data transformation that has objective partitioning. partitioning data transformation A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. partitioning objective A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. class discovery data transformation A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. class discovery objective A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. class prediction objective A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. cross validation objective A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. clustered data visualization A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. study design A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities quality (PATO) PATO:0000072 trait quality PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. composed of compositionality content structure, composition composition A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. concentration concentration of A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. Wikipedia:http://en.wikipedia.org/wiki/concentration A quality that is the extent of space between two entities. distance A quality that is the extent of space between two entities. PATOC:GVG A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time. frequency A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time. Wikipedia:http://en.wikipedia.org/wiki/frequency A physical quality inhering in a bearer by virtue of the bearer's resistance to pressure, being broken, or pierced impenetrability toughness hardness A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. PATOC:GVG 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). 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). PATOC:GVG qualitative A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. deviation (from_normal) deviation(from_normal) A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. size A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. WordNet:WordNet A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. PATOC:GVG A physical quality inhering in a bearer that has mass near a gravitational body. weight A physical quality inhering in a bearer that has mass near a gravitational body. Wikipedia:http://en.wikipedia.org/wiki/Weight A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. 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. PATOC:GVG 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. 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. PATOC:GVG conformation VT:1000738 A physical quality of the thermal energy of a system. temperature A physical quality of the thermal energy of a system. PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. rate A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. PATOC:melissa A quality in which events occur in sequence. time A quality in which events occur in sequence. PATOC:GVG An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. behavioral quality A hardness quality of being rigid and resistant to pressure. firm impenetrable tough hard A size quality which is relatively low. hypoplasia underdeveloped reduced small tiny decreased size An optical quality which obtains by virtue of the ability of the bearer to absorb visible light. opacity An optical quality which obtains by virtue of the ability of the bearer to absorb visible light. PATOC:GVG A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy. non-transparent clouding cloudy opaque 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). permeability 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. A structure quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices. porosity A structure quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices. PATOC:GVG 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. porous A physical quality of a liquid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow. viscosity A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity. viscous A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. 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. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum. force amplitude force A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum. thesaurus.maths:thesaurus.maths A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width. elongated A quality which inheres in an process. quality of a process quality of occurrent quality of process relational quality of occurrent process quality A quality which inheres in an process. PATOC:GVG A physical object quality which inheres in a single-bearer. quality of a single physical entity true A quality which inheres in a continuant. 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. PATOC:GVG A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. electromagnetic (EM) radiation quality A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. Wikipedia:http://en.wikipedia.org/wiki/Electromagnetic_radiation An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. optical quality An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. PATOC:GVG A temperature which is relatively low. cold low temperature decreased temperature A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. period time duration A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATOC:mellybelly A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology. amorphous A position which is relatively high. high position increased position A positional which is relatively low. low position decreased position A shape quality inhering in a bearer by virtue of the bearer's having an oblique or slanted direction. sloped A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. solidity quality of a solid A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. gaseous quality of a gas A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. Chemistry:http://chemistry.about.com/od/chemistryglossary/a/gasdefinition.htm PATOC:GVG A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. liquidity quality of a liquid A mass which is higher than normal or average. high mass large mass increased mass A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per liter of solution. osmolarity A osmolarity which is relatively high. high osmolarity increased osmolarity A positional quality inhering in a bearer by virtue of the bearer's vertical distance of a point above or below a reference surface. 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. Trailillustrated:Trailillustrated An elevation which is relatively high. high elevation elevated increased elevation An elevation which is relatively low. low elevation decreased elevation A viscosity which relatively high. high viscosity increased viscosity A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. 1-D size 1-D extent A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. PATOC:GVG A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. 3D size 3-D extent A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. PATOC:GVG A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. radiation quality A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. PATOC:GVG A composition quality inhering in a bearer by virtue of the bearer's containing granules. granular A quality inhering in a bearer by virtue of whether the bearer's being covered by a liquid. wetness A quality inhering in a bearer by virtue of whether the bearer's being covered by a liquid. wordreference.com:wordreference.com A wetness quality inhering in a bearer by virtue of the bearer's being covered by a liquid. wet A wetness quality inhering in a bearer by virtue of the bearer's being covered by a liquid. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. frozen A quality that inheres in an entire organism or part of an organism. organismal quality A quality that inheres in an entire organism or part of an organism. PATOC:CJM physical quality of a process A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. laminar sloped downward A positional quality inhering in a bearer by virtue the bearer's being changed in position. displaced A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. relational molecular quality molecular quality A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. PATOC:GVG A quality inhering in a bearer by virtue of its constitution. quality of a substance A quality inhering in a bearer by virtue of its constitution. PATOC:GVG A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. handedness Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. left handedness Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. right handedness Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot. ambidextrous handedness A quality that has a value that is increased compared to normal or average. increased quality A quality that has a value that is decreased compared to normal or average. decreased quality A quality of an object that has a value that is decreased compared to normal or average. decreased object quality A quality of an object that has a value that is increased compared to normal or average. increased object quality The number of repeated events per unit time, occurring in a repeating series. (e.g. the number of heart beats occurring over 1 minute) rate of occurence The number of repeated events per unit time, occurring in a repeating series. (e.g. the number of heart beats occurring over 1 minute) https://orcid.org/0000-0002-9943-9018 2 Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. A material entity that consists of two or more organisms, viruses, or viroids. A material entity that consists of two or more organisms, viruses, or viroids. group of organism organism collection May be of the same or different species. collection of organisms collection of organisms This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed. A collection of organisms, all of the same species, that live in the same place. ISBN:0878932739 It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. population of organisms 2 A community of at least two different species, living in a particular area. Must have at least two populations of different species as members. A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. multispecies community ISBN:0865423504 envoPolar Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. ecological community A collection of organisms that has as parts every organism of given species and no organisms of any other species. At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible. This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. species as a collection of organisms 1 2 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. collection of organisms of the same species single-species collection of organisms A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. community A collection of organisms that consists of two or more organisms from at least two species. Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". multi-species collection of organisms A material entity that is one or more organisms, viruses or viroids. organismal entity A plant experimental condition (PECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (PECO:0007357) or the combinatorial application thereof. plant treatment (narrow) plant exposure A plant experimental condition (PECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (PECO:0007357) or the combinatorial application thereof. PECO:cooperl A plant exposure (PECO:0001001) and/or study type (PECO:0007231) applied to a whole plant (PO:0000003), a plant structure (PO:00090119), and/or a plant population as part of an experiment to evaluate the plant response. plant treatment ontology (related) treatment ontology (related) plant experimental condition A plant exposure (PECO:0001001) and/or study type (PECO:0007231) applied to a whole plant (PO:0000003), a plant structure (PO:00090119), and/or a plant population as part of an experiment to evaluate the plant response. Gramene:pankaj_jaiswal PECO:cooperl A plant structure (PO:0005679) which is a whole organism. genet (broad) ramet (broad) PO_GIT:538 PO_GIT:69 planta entera (Spanish, exact) 植物体全体 (Japanese, exact) bush (narrow) frutex (narrow) frutices (narrow) gametophyte (narrow) herb (narrow) liana (narrow) prothalli (narrow) prothallium (narrow) prothallus (narrow) seedling (narrow) shrub (narrow) sporophyte (narrow) suffrutex (narrow) suffrutices (narrow) tree (narrow) vine (narrow) woody clump (narrow) plant_anatomy clonal colony (related) colony (related) PO:0000003 Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280). whole plant A plant structure (PO:0005679) which is a whole organism. POC:curators planta entera (Spanish, exact) POC:Maria_Alejandra_Gandolfo 植物体全体 (Japanese, exact) NIG:Yukiko_Yamazaki frutex (narrow) FNA:e4dde193-57f7-4ab9-9d25-96b4ca0088ba frutices (narrow) FNA:ec8c2064-2a67-43d7-8e14-aecfef5cf33b prothalli (narrow) FNA:4b610104-1bb0-4c6b-9bb9-e3cc61d11ac0 prothallus (narrow) FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8 suffrutex (narrow) FNA:99508f62-7116-4e2b-90c0-19ff55ebd967 suffrutices (narrow) FNA:ba1b1bd5-75bd-4195-b11c-3aba08da08c2 woody clump (narrow) FNA:c1ccca7d-2a98-4a9d-8603-c34b551935e0 A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. An anatomical structure that is or was part of a plant, or was derived from a part of a plant. PO_GIT:57 estructura vegetal (Spanish, exact) 植物 構造 (Japanese, exact) plant_anatomy PO:0009011 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. plant structure A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. CARO:0000003 POC:curators estructura vegetal (Spanish, exact) POC:Maria_Alejandra_Gandolfo 植物 構造 (Japanese, exact) NIG:Yukiko_Yamazaki 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. PO:cooperl An anatomical entity that is or was part of a plant. rwalls 2010-11-15T11:41:38Z PO_GIT:224 entidad anat&#243mica vegetal (Spanish, exact) 植物 解剖学（形態）的実体 (Japanese, exact) plant_anatomy PO:0025131 Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. plant anatomical entity cjm An anatomical entity that is or was part of a plant. BFO:0000004 CARO:0000000 POC:curators entidad anat&#243mica vegetal (Spanish, exact) POC:Maria_Alejandra_Gandolfo 植物 解剖学（形態）的実体 (Japanese, exact) NIG:Yukiko_Yamazaki Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. CAROC:Brownsville2014 A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 Chris Mungall http://www.jbiomedsem.com/content/4/1/43 system root node Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. anatomical entity A unit of measurement is a standardized quantity of a physical quality. "A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia] unit A unit of measurement is a standardized quantity of a physical quality. Wikipedia:Wikipedia A unit which is a standard measure of the distance between two points. "A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia] length unit A unit which is a standard measure of the distance between two points. Wikipedia:Wikipedia A unit which is a standard measure of the amount of matter/energy of a physical object. "A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia] mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. Wikipedia:Wikipedia A unit which is a standard measure of the dimension in which events occur in sequence. time derived unit "A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia] time unit A unit which is a standard measure of the dimension in which events occur in sequence. Wikipedia:Wikipedia "A unit which is a standard measure of the flow of electric charge." [Wikipedia:Wikipedia] electric current unit A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. temperature derived unit "A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [Wikipedia:Wikipedia] temperature unit A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. Wikipedia:Wikipedia A unit which is a standardised quantity of an element or compound with uniform composition. "A unit which is a standardised quantity of an element or compound with uniform composition." [Wikipedia:Wikipedia] substance unit "A unit which is a standard measure of the wavelength-weighted power emitted by a light source in a particular direction." [Wikipedia:Wikipedia] luminous intensity unit "A unit which is one of a particular measure to which all measures of that type can be related." [NIST:NIST] base unit prefix "A unit which is a standard measure of the amount of a 2-dimensional flat surface." [UOC:GVG] area unit "A unit which is a standard measure of the rate of change of velocity in either speed or direction." [Wikipedia:Wikipedia] acceleration unit "A unit which is a standard measure of the rate of angular movement about an axis; the angle rotated in a given time." [Wikipedia:Wikipedia] angular velocity unit "A unit which is a standard measure of the rate of change of angular velocity." [Wikipedia:Wikipedia] angular acceleration unit A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. "A unit which represents a standard measurement of how much of a given substance there is mixed with another substance." [UOC:GVG] concentration unit A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. UOC:GVG "A density unit which is a standard measure of the mass of a substance in a given volume." [UOC:GVG] mass density unit "A unit which is a standard measure of the luminous intensity impinging on a given area." [Wikipedia:Wikipedia] luminance unit "A density unit which is a standard measure of the mass exerting an influence on a given area." [Wikipedia:Wikipedia] area density unit "A unit which is a standard measure of the mass of a homogeneous substance containing 6.02 x 1023 atoms or molecules." [Wikipedia:Wikipedia] molar mass unit "A unit which is a standard measure of the volume of a homogeneous substance containing 6.02 x 1023 atoms or molecules." [Wikipedia:Wikipedia] molar volume unit "A unit which is a standard measure of the quantity of motion measured by the product of mass and velocity." [Wikipedia:Wikipedia] momentum unit "A unit which is a standard measure of the number of rotations in a given time." [NIST:NIST] rotational frequency unit "A unit which is a standard measure of the volume of a given mass of substance (the reciprocal of density)." [Wikipedia:Wikipedia] specific volume unit "A unit which is a standard measure of the rate of movement. Speed is measured in the same physical units of measurement as velocity, but does not contain the element of direction that velocity has. Speed is thus the magnitude component of velocity." [Wikipedia:Wikipedia] speed/velocity unit "A concentration unit which is a standard measure of the number of moles of a given substance per liter of solution." [UOC:GVG] unit of molarity "A concentration unit which is a standard measure of the number of moles of a given substance per kilogram of solvent." [UOC:GVG] unit of molality "A unit of concentration which highlights the chemical nature of salts." [Wikipedia:Wikipedia] unit of normality A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST] volume unit A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. NIST:NIST A unit which is a standard measure of the number of repetitive actions in a particular time. "A unit which is a standard measure of the number of repetitive actions in a particular time." [NIST:NIST] frequency unit A unit which is a standard measure of the number of repetitive actions in a particular time. NIST:NIST "A unit which is a standard measure of the force is applied when a mass is accelerated." [NIST:NIST] force unit "A unit which is a standard measure of the force applied to a given area." [NIST:NIST] pressure unit "A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc)." [NIST:NIST] energy unit "A unit which is a standard measure power or the rate of doing work." [NIST:NIST] power unit "A unit which is a standard measure of the luminous flux incident on a unit area." [Wikipedia:Wikipedia] illuminance unit "A unit which is a standard measure of the flow of radiant energy." [Wikipedia:Wikipedia] luminous flux unit "A unit which is a standard measure of the amount of the action of a catalyst." [NIST:NIST] catalytic activity unit "A unit which is a standard measure of the figure or space formed by the junction of two lines or planes." [Wikipedia:Wikipedia] angle unit "A unit which is a standard measure of the angle formed by two straight lines in the same plane." [Wikipedia:Wikipedia] plane angle unit "A unit which is a standard measure of the angle formed by three or more planes intersecting at a common point." [Wikipedia:Wikipedia] solid angle unit "A unit which is a standard measure of the amount of radiation emitted by a given radiation source as well as the amount of radiation absorbed or deposited in a specific material by a radiation source." [OCRBS:OCRBS] radiation unit "A unit which is a standard measure of the transformation (disintegration) rate of a radioactive substance." [DEFRA:DEFRA] activity (of a radionuclide) unit "A unit which is a standard measure of the energy imparted by ionizing radiation to unit mass of matter such as tissue." [DEFRA:DEFRA] absorbed dose unit "A unit which is a standard measure of the expression of dose in terms of its biological effect." [ORCBS:ORCBS] dose equivalent unit "A unit which is a standard measure of the quantity that expresses the ability of radiation to ionize air and thereby create electric charges which can be collected and measured." [ORCBS:ORCBS] exposure unit "A unit which is a standard measure of the power of electromagnetic radiation at a surface, per unit area." [Wikipedia:Wikipedia] irradiance unit "A unit which is a standard measure of the intensity of light." [NIST:NIST] light unit "A unit which is a standard measure of the intensity of electromagnetic radiation." [Wikipedia:Wikipedia] radiant intensity unit "A unit which is a standard measure of the power of electromagnetic radiation through space or through a material medium in the form of electromagnetic waves." [Wikipedia:Wikipedia] radiance unit "A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance." [Wikipedia:Wikipedia] parts per notation unit "A concentration unit which is a standard measure of the number of units, as an agreed arbitrary amount, of a given substance per a specific volume of solution." [Webmd:Webmd] unit per volume unit "A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia] density unit "A density unit which is a standard measure of the mass exerting an influence on a one-dimensional object." [Wikipedia:Wikipedia] linear density unit "A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia] dimensionless unit "A dimensionless ratio unit which denotes numbers as fractions of 100." [Wikipedia:Wikipedia] percent "A dimensionless unit which denotes a simple count of things." [MGED:MGED] count unit "A dimensionless unit which denotes an amount or magnitude of one quantity relative to another." [Wikipedia:Wikipedia] ratio "A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator)." [Wikipedia:Wikipedia] fraction "A concentration unit which denotes the average cell number in a given volume." [Bioedonline:Bioedonline] cell concentration unit "A concentration unit which is a standard measure of the amount of the action of a catalyst in a given volume." [UOC:GVG] catalytic (activity) concentration unit "A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution." [NIST:NIST] volume per unit volume "A concentration unit which a measure of plague forming units in a given volume." [UOC:GVG] plaque forming unit per volume "A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field." [Wikipedia:Wikipedia] electric potential difference unit "A unit which is a standard measure of the quantity of unbalanced electricity in a body (either positive or negative) and construed as an excess or deficiency of electrons." [WordNet:WordNet] electric charge "A unit which is a standard measure of quantity of magnetism, taking account of the strength and the extent of a magnetic field." [Wikipedia:Wikipedia] magnetic flux unit "A unit which is a standard measure of the strength of a magnetic field." [allnet:allnet] magnetic flux density unit "A unit which is a standard measure of the amount of information." [Wikipedia:Wikipedia] information unit "An information unit which is a standard measure of the detail an image holds." [Wikipedia:Wikipedia] image resolution unit "An image resolution unit which is a standard measure of the way luminance and chrominance may be sampled at different levels." [Wikipedia:Wikipedia] spatial resolution unit "A unit which is a standard measure of the ability of a liguid to attraction of molecules at its surface as a result of unbalanced molecular cohesive forces." [NIST:NIST] surface tension unit "A unit which is a standard measure of the internal resistance of fluids to flow." [UOC:GVG] viscosity unit "A unit which represents a standard measurement of the transmission of an entity through a medium." [UOC:GVG] conduction unit "A unit which represents a standard measurement of the movement of electrically charged particles through a transmission medium (electrical conductor)." [UOC:GVG] electrical conduction unit "A unit which represents a standard measurement of the spontaneous transfer of thermal energy through matter, from a region of higher temperature to a region of lower temperature." [Wikipedia:Wikipedia] heat conduction unit "The electric field strength is a unit which is a measure of the potential difference between two points some distance apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field] electric field strength unit A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time . "A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time ." [Wikipedia:Wikipedia] volumetric flow rate unit A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time . Wikipedia:Wikipedia A unit which represents a standard measurement occurrence of a process per unit time. "A unit which represents a standard measurement occurrence of a process per unit time." [UOC:GVG] rate unit "A prefix in the metric system denoting a factor of million." [UO:GVG] mega "A prefix in the metric system denoting a factor of one thousand." [UO:GVG] kilo "A prefix in the metric system denoting a factor of one tenth." [UO:GVG] deci "A prefix in the metric system denoting a factor of one thousand." [UO:GVG] milli "A prefix in the metric system denoting a factor of one hundred." [UO:GVG] centi "A prefix in the metric system denoting a factor of 10 to the power of -6." [UO:GVG] micro "A prefix in the metric system denoting a factor of 10 to the power of -9." [UO:GVG] nano "A prefix in the metric system denoting a factor of 10 to the power of -12." [GVG:UO] pico "A prefix in the metric system denoting a factor of 10 to the power of -15." [UO:GVG] femto "A prefix in the metric system denoting a factor of 10 to the power of -18." [UO:GVG] atto "A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered to a recipient subject, expressed in terms of the size of the subject." [UO:PC] dose unit meter based unit second based unit ampere based unit kelvin based unit mole based unit candela based unit angstrom based unit gram based unit degree Celsius based unit minute based unit hour based unit day based unit week based unit month based unit year based unit molar based unit molal based unit normal based unit mole fraction based unit meter per second per second based unit radian per second per second based unit radian per second based unit square meter based unit square centimeter based unit square millimeter based unit gram per cubic centimeter based unit candela per square meter based unit gram per mole based unit cubic meter per mole based unit cubic centimeter per mole based unit turns per second based unit cubic meter per kilogram based unit meter per second based unit cubic meter based unit cubic centimeter based unit liter based unit cubic decimeter based unit hertz based unit newton based unit pascal based unit joule based unit watt based unit lux based unit lumen based unit katal based unit radian based unit steradian based unit becquerel based unit curie based unit gray based unit rad based unit roentgen based unit sievert based unit Roentgen equivalent man based unit disintegrations per minute based unit counts per minute based unit century based unit half life based unit foot candle based unit watt per square meter based unit einstein per square meter per second based unit watt per steradian per square meter based unit watt per steradian based unit mass percentage based unit mass volume percentage based unit volume percentage based unit parts per hundred based unit parts per thousand based unit parts per million based unit parts per billion based unit parts per trillion based unit parts per quadrillion based unit gram per milliliter based unit gram per liter based unit unit per milliliter based unit unit per liter based unit mass per unit volume based unit enzyme unit based unit degree based unit pi based unit molecule count based unit purity percentage based unit confluence percentage based unit degree Fahrenheit based unit pH based unit liter per kilogram based unit cells per milliliter based unit katal per cubic meter based unit katal per liter based unit gram per deciliter based unit colony forming unit based unit plaque forming unit based unit colony forming unit per milliliter based unit plaque forming unit per milliliter based unit disintegrations per second based unit volt based unit coulomb based unit dalton based unit watt-hour based unit weber based unit tesla based unit volt-hour based unit bit based unit byte based unit chroma sampling unit based unit dynamic range unit based unit dots per inch based unit pixels per inch based unit pixels per millimeter based unit base pair based unit kibibyte based unit mebibyte based unit newton per meter based unit dyne per cm based unit pascal second based unit poise based unit effective dose unit based unit siemens based unit watt per meter kelvin based unit electronvolt based unit volt per meter based unit absorbance unit based unit count per nanomolar second based unit count per molar second based unit count per nanomolar based unit count per molar based unit dosage unit based unit relative light unit based unit relative luminescence unit based unit relative fluorescence unit based unit square micrometer based unit hectare based unit inch based unit thou based unit foot based unit yard based unit chain based unit furlong based unit mile based unit league based unit maritime length unit based unit fathom based unit cable based unit nautical mile based unit perch based unit rood based unit acre based unit fluid ounce based unit gill based unit pint based unit quart based unit gallon based unit grain based unit drachm based unit ounce based unit pound based unit stone based unit quarter based unit hundredweight based unit ton based unit slug based unit teaspoon based unit gram per square meter based unit A state of being, an external or environmental factor or a treatment observed or administered prior to or concurrent with an investigative procedure such as an assessment of a morphological or physiological state or property in a single individual or sample or in a group of individuals or samples, especially a state, factor or treatment which has the potential to influence the outcome of such an assessment. experimental condition A state of being, an external or environmental factor or a treatment observed or administered prior to or concurrent with an investigative procedure such as an assessment of a morphological or physiological state or property in a single individual or sample or in a group of individuals or samples, especially a state, factor or treatment which has the potential to influence the outcome of such an assessment. Multiple_Dictionaries:http://www.thefreedictionary.com/ PMID:22654893 http://orcid.org/0000-0002-4366-3088 2019-03-05T17:25:21Z Western Australia Ecoregion WWF:AA1310 https://www.worldwildlife.org/ecoregions/aa1310 Western Australian Mulga Shrublands Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-05T17:51:32Z https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands Australasia Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-05T17:52:41Z Southern central Australia Ecoregion WWF:AA1309 https://www.worldwildlife.org/ecoregions/aa1309 Tirari-Sturt Stony Desert Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-05T17:54:35Z Eastern central Australia Ecoregion WWF:AA1308 https://www.worldwildlife.org/ecoregions/aa1308 Simpson Desert Region http://orcid.org/0000-0002-4366-3088 2019-03-05T17:56:13Z Western Australia Ecoregion WWF:AA1307 https://www.worldwildlife.org/ecoregions/aa1307 Pilbara Shrublands Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-05T18:10:52Z Western coast of Australia Ecoregion WWF:AA1301 https://www.worldwildlife.org/ecoregions/aa1301 Carnarvon Xeric Shrublands Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-05T18:12:28Z Central Australia Ecoregion WWF:AA1302 https://www.worldwildlife.org/ecoregions/aa1302 Central Ranges Xeric Shrub Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-05T18:15:11Z Western central Australia WWF:AA1303 https://www.worldwildlife.org/ecoregions/aa1303 Gibson Desert Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-05T18:17:15Z Northwestern Australia WWF:AA1304 https://www.worldwildlife.org/ecoregions/aa1304 The Great Sandy-Tanami Desert Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-05T18:24:06Z Southern Australia Ecoregion WWF:AA1305 https://www.worldwildlife.org/ecoregions/aa1305 Great Victoria Desert Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-05T18:26:16Z Southern Australia Ecoregion WWF:AA1306 https://www.worldwildlife.org/ecoregions/aa1306 Nullarbor Plains Xeric Shrubland Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:01:41Z https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands Afrotropical Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:02:37Z Southern Africa: Southern Namibia into South Africa WWF:AT1322 https://www.worldwildlife.org/ecoregions/at1322 Succulent Karoo Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:07:38Z WWF:AT1321 https://www.worldwildlife.org/ecoregions/at1321 Arabian Peninsula: Yemen and Saudi Arabia Yemen and Saudi Arabia Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:11:38Z WWF:AT1320 https://www.worldwildlife.org/ecoregions/at1320 Arabian Peninsula: Yemen, Saudi Arabia, and Oman Yemen, Saudi Arabia, and Oman Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:13:00Z WWF:AT1319 https://www.worldwildlife.org/ecoregions/at1319 Somali montane xeric woodlands ecoregion Somali Montane Xeric Woodland Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:15:07Z Islands east of the Horn of Africa and south of Yemen Ecoregion WWF:AT1318 https://www.worldwildlife.org/ecoregions/at1318 Socotran Archipelago Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:18:55Z WWF:AT1317 https://www.worldwildlife.org/ecoregions/at1317 Red Sea Coastal Desert Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:20:56Z WWF:AT1316 https://www.worldwildlife.org/ecoregions/at1316 Namibian Savanna Woodland Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:24:28Z Africa: Namibia Ecoregion WWF:AT1315 https://www.worldwildlife.org/ecoregions/at1315 Namib Desert Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:26:15Z WWF:AT1314 https://www.worldwildlife.org/ecoregions/at1314 Nama Karoo Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:28:43Z WWF:AT1313 https://www.worldwildlife.org/ecoregions/at1313 Masai Xeric Grasslands and Shrublands Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:30:23Z WWF:AT1312 https://www.worldwildlife.org/ecoregions/at1312 Madagascar Succulent Woodlands Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:31:29Z WWF:AT1311 https://www.worldwildlife.org/ecoregions/at1311 Madagascar spiny desert ecoregion Madagascar Spiny Thickets Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:39:32Z WWF:AT1310 https://www.worldwildlife.org/ecoregions/at1310 Africa: Coastal Namibia and Angola Ecoregion Kaokoveld Desert Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:42:47Z WWF:AT1309 https://www.worldwildlife.org/ecoregions/at1309 Kalahari Xeric Savanna Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:44:54Z WWF:AT1308 https://www.worldwildlife.org/ecoregions/at1308 Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion Ile Europa and Bassas da India Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:46:58Z Eastern Africa: Somalia WWF:AT1307 https://www.worldwildlife.org/ecoregions/at1307 Hobyo Grassland and Shrubland Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-06T22:54:57Z WWF:AT1306 https://www.worldwildlife.org/ecoregions/at1306 Arabian Peninsula: Oman and United Arab Emirates Ecoregion Oman and United Arab Emirates Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-07T00:08:06Z WWF:AT1305 https://www.worldwildlife.org/ecoregions/at1305 Ethiopian Xeric Grasslands and Shrublands Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-07T00:11:29Z WWF:AT1304 https://www.worldwildlife.org/ecoregions/at1304 Eritrean Coastal Desert Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-07T00:13:33Z WWF:AT1303 https://www.worldwildlife.org/ecoregions/at1303 North central Africa: Eastern Chad and small area of western Sudan East Saharan Montane Xeric Woodland Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-07T00:16:12Z WWF:AT1302 https://www.worldwildlife.org/ecoregions/at1302 Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion Oman, Yemen, and Saudi Arabia Ecoregion http://orcid.org/0000-0002-4366-3088 2019-03-07T00:18:09Z WWF:AT1301 https://www.worldwildlife.org/ecoregions/at1301 Aldabra Island Xeric Scrub Ecoregion example to be eventually removed The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot core placeholder removed An editor note should explain what were the merged terms and the reason for the merge. terms merged This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. We expect to be able to mine these new reasons and add instances as required. other true Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion third planet from the Sun in the Solar System Earth third planet from the Sun in the Solar System https://www.wikidata.org/wiki/Q2 "Suni, or Jalca, is one of the eight Natural Regions of Peru. It is located in the Andes at an altitude between 3,500 and 4,000 metres above sea level. Suni has a dry and cold weather and there are many glacial valleys. The flora includes gramineous plants and shrubs such as the taya-taya (Caesalpinia spinosa), the quishuar (Buddleja coriacea), and the cantuta (Cantua buxifolia) which was considered sacred by the Incas. Even though it is hard for plants to grow because of the weather, people are able to cultivate such crops as quinoa, qañiwa, broad beans and ulluku (Ullucus tuberosus). The main fauna is the guinea pig and, among numerous other highland birds, the Chiguanco thrush." Jalca Suni "Suni, or Jalca, is one of the eight Natural Regions of Peru. It is located in the Andes at an altitude between 3,500 and 4,000 metres above sea level. Suni has a dry and cold weather and there are many glacial valleys. The flora includes gramineous plants and shrubs such as the taya-taya (Caesalpinia spinosa), the quishuar (Buddleja coriacea), and the cantuta (Cantua buxifolia) which was considered sacred by the Incas. Even though it is hard for plants to grow because of the weather, people are able to cultivate such crops as quinoa, qañiwa, broad beans and ulluku (Ullucus tuberosus). The main fauna is the guinea pig and, among numerous other highland birds, the Chiguanco thrush." https://en.wikipedia.org/wiki/Suni_(geography) Earth's interconnected water system World Ocean Earth's interconnected water system https://www.wikidata.org/wiki/Q715269 metre m meter A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. "A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." [BIPM:BIPM, NIST:NIST] A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. BIPM:BIPM NIST:NIST A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. kg kilogram "A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France." [BIPM:BIPM, NIST:NIST] A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. BIPM:BIPM NIST:NIST s second "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom." [BIPM:BIPM, NIST:NIST] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. BIPM:BIPM NIST:NIST "An electric current unit which is equal to the constant current which, if maintained in two straight parallel conductors of infinite length, of negligible circular cross-section, and placed 1 m apart in vacuum, would produce between these conductors a force equal to 2 x 10^[-7] newton per meter of length." [BIPM:BIPM, NIST:NIST] ampere "A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water." [BIPM:BIPM, NIST:NIST] kelvin "A substance unit which is equal to the amount of substance of a molecular system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12." [BIPM:BIPM, NIST:NIST] mole "A luminous intensity unit which equal to the luminous intensity, in a given direction, of a source that emits monochromatic radiation of frequency 540 x 1012 hertz and that has a radiant intensity in that direction of 1/683 watt per steradian." [BIPM:BIPM, NIST:NIST] candela centimeter cm centimetre "A length unit which is equal to one hundredth of a meter or 10^[-2] m." [NIST:NIST] A length unit which is equal to one hundredth of a meter or 10^[-2] m. A length unit which is equal to one hundredth of a meter or 10^[-2] m. NIST:NIST micrometre A length unit which is equal to one thousandth of a meter or 10^[-3] m. mm millimeter "A length unit which is equal to one thousandth of a meter or 10^[-3] m." [NIST:NIST] A length unit which is equal to one thousandth of a meter or 10^[-3] m. NIST:NIST "A length unit which is equal to one millionth of a meter or 10^[-6] m." [NIST:NIST] micrometer nanometer "A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." [NIST:NIST] angstrom "A length unit which is equal to 10 [-10] m." [NIST:NIST] picometer "A length unit which is equal to 10^[-12] m." [NIST:NIST] A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. gram g "A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg." [NIST:NIST] A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. NIST:NIST milligram A mass unit which is equal to one thousandth of a gram or 10^[-3] g. "A mass unit which is equal to one thousandth of a gram or 10^[-3] g." [UOC:GVG] mg A mass unit which is equal to one thousandth of a gram or 10^[-3] g. UOC:GVG "A mass unit which is equal to one millionth of a gram or 10^[-6] g." [UOC:GVG] microgram "A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g." [UOC:GVG] nanogram "A mass unit which is equal to 10^[-12] g." [UOC:GVG] picogram "A mass unit which is equal to 10^[-15] g." [NIST:NIST] femtogram degree Celsius "A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K." [NIST:NIST] A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. C A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. NIST:NIST "A time unit which is equal to one thousandth of a second or 10^[-3] s." [NIST:NIST] millisecond microsecond "A time unit which is equal to one millionth of a second or 10^[-6] s." [NIST:NIST] picosecond "A time unit which is equal to 10^[-12] s." [NIST:NIST] min A time unit which is equal to 60 seconds. minute "A time unit which is equal to 60 seconds." [Wikipedia:Wikipedia] A time unit which is equal to 60 seconds. Wikipedia:Wikipedia A time unit which is equal to 3600 seconds or 60 minutes. hour h "A time unit which is equal to 3600 seconds or 60 minutes." [Wikipedia:Wikipedia] A time unit which is equal to 3600 seconds or 60 minutes. Wikipedia:Wikipedia A time unit which is equal to 24 hours. "A time unit which is equal to 24 hours." [Wikipedia:Wikipedia] day A time unit which is equal to 24 hours. Wikipedia:Wikipedia A time unit which is equal to 7 days. week "A time unit which is equal to 7 days." [Wikipedia:Wikipedia] A time unit which is equal to 7 days. Wikipedia:Wikipedia A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. month "A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days." [Wikipedia:Wikipedia] A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. Wikipedia:Wikipedia A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days. "A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days." [Wikipedia:Wikipedia] year A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days. Wikipedia:Wikipedia "An electric current unit current which is equal to one thousandth of an ampere or 10^[-3] A." [UOC:GVG] milliampere microampere "An electric current unit current which is equal to one millionth of an ampere or 10^[-6] A." [UOC:GVG] "A substance unit equal to a millionth of a mol or 10^[-6] mol." [NIST:NIST] micromole millimole "A substance unit equal to a thousandth of a mol or 10^[-3] mol." [NIST:NIST] "A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol." [NIST:NIST] nanomole "A substance unit equal to 10^[-12] mol." [NIST:NIST] picomole femtomole "A substance unit equal to 10^[-15] mol." [NIST:NIST] attomole "A substance unit equal to 10^[-18] mol." [NIST:NIST] "A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L)." [UOC:GVG] molar millimolar "A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M." [UOC:GVG] micromolar "A unit of molarity which is equal to one millionth of a molar or 10^[-6] M." [UOC:GVG] "A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M." [UOC:GVG] nanomolar "A unit of molarity which is equal to 10^[-12] M." [UOC:GVG] picomolar molal "A unit of concentration which expresses a concentration of a solution of 1 mole per kilogram of solvent (mol/kg)." [UOC:GVG] millimolal "A molality unit which is equal to one thousandth of a molal or 10^[-3] m." [UOC:GVG] micromolal "A molality unit which is equal to one millionth of a molal or 10^[-6] m." [UOC:GVG] nanomolal "A molality unit which is equal to one thousandth of one millionth of a molal or 10^[-9] m." [UOC:GVG] picomolal "A molality unit which is equal to 10^[-12] m." [UOC:GVG] femtomolar "A unit of molarity which is equal to 10^[-15] M." [UOC:GVG] normal "A unit of concentration which is one gram equivalent of a solute per liter of solution. A gram equivalent weight or equivalent is a measure of the reactive capacity of a given molecule." [Wikipedia:Wikipedia] mole fraction "A concentration unit which denotes the number of moles of solute as a proportion of the total number of moles in a solution." [Wikipedia:Wikipedia] meter per second per second "An acceleration unit which is equal to the acceleration an object changing its velocity by 1meter/s over a time period that equals one second." [NIST:NIST] "An angular unit acceleration which is equal to the angular acceleration of an object changing its angular velocity by 1rad/s over a time period that equals one second." [NIST:NIST] radian per second per second "An angular unit velocity which is equal to about 9.54930 rpm (revolutions per minute)." [NIST:NIST] radian per second "An area unit which is equal to an area enclosed by a square with sides each 1 meter long." [NIST:NIST] square meter "An area unit which is equal to one ten thousandth of a square meter or 10^[-4] m^[2]." [NIST:NIST] square centimeter square millimeter "An area unit which is equal to one millionth of a square meter or 10^[-6] m^[2]." [NIST:NIST] "A mass unit density which is equal to mass of an object in kilograms divided by the volume in cubic meters." [UOC:GVG] kilogram per cubic meter gram per cubic centimeter "A mass unit density which is equal to mass of an object in grams divided by the volume in cubic centimeters." [UOC:GVG] candela per square meter "A luminance unit which is equal to a luminous intensity of one candela radiating from a surface whose area is one square meter." [NIST:NIST] "An area density unit which is equal to the mass of an object in kilograms divided by the surface area in meters squared." [NIST:NIST] kilogram per square meter "A molar mass unit which is equal to one kilogram of mass of one mole of chemical element or chemical compound." [NIST:NIST] kilogram per mole "A molar mass unit which is equal to one gram of mass of one mole of chemical element or chemical compound." [NIST:NIST] gram per mole cubic meter per mole "A molar volume unit which is equal to 1 cubic meter occupied by one mole of a substance in the form of a solid, liquid, or gas." [NIST:NIST] cubic centimeter per mole "A molar volume unit which is equal to 1 cubic centimeter occupied by one mole of a substance in the form of a solid, liquid, or gas." [NIST:NIST] "A momentum unit which is equal to the momentum of a one kilogram mass object with a speed of one meter per second." [NIST:NIST] kilogram meter per second "A rotational frequency unit which is equal to the number complete turn in a period of time that equals to 1 second." [NIST:NIST] turns per second "A specific volume unit which is equal to one cubic meter volume occupied by one kilogram of a particular substance." [NIST:NIST] cubic meter per kilogram meter per second "A speed/velocity unit which is equal to the speed of an object traveling 1 meter distance in one second." [NIST:NIST] cubic meter "A volume unit which is equal to the volume of a cube with edges one meter in length. One cubic meter equals to 1000 liters." [NIST:NIST] cubic centimeter "A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml." [NIST:NIST] milliliter "A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter." [NIST:NIST] A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. millilitre ml A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. NIST:NIST litre A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. "A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter." [NIST:NIST] L l liter A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. NIST:NIST "A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L." [NIST:NIST] cubic decimeter microliter "A volume unit which is equal to one millionth of a liter or 10^[-6] L." [NIST:NIST] nanoliter "A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L." [NIST:NIST] picoliter "A volume unit which is equal to 10^[-12] L." [NIST:NIST] femtoliter "A volume unit which is equal to 10^[-15] L." [NIST:NIST] "A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second." [NIST:NIST] hertz "A force unit which is equal to the force required to cause an acceleration of 1m/s2 of a mass of 1 Kg in the direction of the force." [NIST:NIST] newton pascal "A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]." [NIST:NIST] joule "An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force." [NIST:NIST] watt "A power unit which is equal to the power used when work is done at the rate of 1 joule per second." [NIST:NIST] lux "An illuminance unit which is equal to the illuminance produced by 1 lumen evenly spread over an area 1 m^[2]." [NIST:NIST] lumen "A luminous flux unit which is equal to the luminous flux emitted into 1 steradian by a point source of 1 candela." [NIST:NIST] katal "A catalytic unit activity which is equal to the activity of a catalyst in moles per second, such as the amount of an enzyme needed to transform one mole of substrate per second." [NIST:NIST] "A plane angle unit which is equal to the angle subtended at the center of a circle by an arc equal in length to the radius of the circle, approximately 57 degrees 17 minutes and 44.6 seconds." [NIST:NIST] radian "A solid angle unit which is equal to the solid angle subtended at the center of a sphere by an area on the surface of the sphere that is equal to the radius squared." [NIST:NIST] steradian becquerel "An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per second or there is one atom disintegration per second (dps)." [NIST:NIST] "An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which there are 3.7 x 10^[10] atom disintegration per second (dps)." [ORCBS:ORCBS] curie "An absorbed dose unit which is equal to the absorption of one joule of radiation energy by one kilogram of matter." [NIST:NIST] gray "An absorbed dose unit which is equal to 0.01 gray (Gy)." [Wikipedia:Wikipedia] rad "An exposure unit which is equal to the amount of radiation required to liberate positive and negative charges of one electrostatic unit of charge in 1 cm^[3] of air at standard temperature and pressure (STP). This corresponds to the generation of approximately 2.0810^[9] ion pairs." [Wikipedia:Wikipedia] roentgen "A dose equivalent unit which is equal to the absorption of one joule of radiation energy by one kilogram of matter." [NIST:NIST] sievert millisievert "A dose equivalent unit which is equal to one thousandth of a sievert or 10^[-3] Sv." [NIST:NIST] "A dose equivalent unit which is equal to one millionth of a sievert or 10^[-6] Sv." [NIST:NIST] microsievert "A dose equivalent unit which when multiplied by hundred is equal to one sievert or 1 Sv. 1 Sv is equal to 100 rem." [Wikipedia:Wikipedia] Roentgen equivalent man microgray "An absorbed dose unit which is equal to one millionth of a gray or 10^[-6] Gy." [NIST:NIST] "An absorbed dose unit which is equal to one thousandth of a gray or 10^[-3] Gy." [NIST:NIST] milligray "An absorbed dose unit which is equal to one thousandth of a millionth of a gray or 10^[-9] Gy." [NIST:NIST] nanogray nanosievert "A dose equivalent unit which is equal to one thousandth of a millionth of a sievert or 10^[-9] Sv." [NIST:NIST] "An activity (of a radionuclide) unit which is equal to one thousandth of a curie or 10^[-3] Ci." [ORCBS:ORCBS] millicurie microcurie "An activity (of a radionuclide) unit which is equal to one millionth of a curie or 10^[-6] Ci." [ORCBS:ORCBS] disintegrations per minute "An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per minute or there is one atom disintegration per minute." [ORCBS:ORCBS] "An activity (of a radionuclide) unit which is equal to the number of light emissions produced by ionizing radiation in one minute." [ORCBS:ORCBS] counts per minute nanosecond "A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s." [NIST:NIST] century "A time unit which is equal to 100 years." [Wikipedia:Wikipedia] half life "A time unit which represents the period over which the activity or concentration of a specified chemical or element falls to half its original activity or concentration." [MGED:MGED] "An illuminance unit which is equal to the illuminance produced by 1 lumen evenly spread over an area 1 foot^[2]. One footcandle is equal to 10.76 lux." [Wikipedia:Wikipedia] foot candle "An irradiance unit which is equal to 1 watt of radiant power incident per one square meter surface area." [NIST:NIST] watt per square meter einstein per square meter per second "An irradiance unit which is equal to one einstein per square meter per second. One einstein is one mole of photons, regardless of their frequency. Therefore, the number of photons in an einstein is Avogadro's number." [Wikipedia:Wikipedia] "A radiance unit which is equal to one watt of radiant power incident per steradian solid angle per one square meter projected area of the source, as viewed from the given direction." [NIST:NIST] watt per steradian per square meter microeinstein per square meter per second "An irradiance unit which is equal to one microeinstein per square meter per second or 10^[-6] microeinstein/sm^[2]." [Wikipedia:Wikipedia] watt per steradian "A radiant intensity unit which is equal to one kilogram meter squared per second cubed per steradian." [NIST:NIST] weight-weight percentage w/w mass percentage A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. "A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture." [Wikipedia:Wikipedia] A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. Wikipedia:Wikipedia mass volume percentage "A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture." [UOC:GVG] volume percentage "A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution." [UOC:GVG] "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 100 regardless of the units of measure as long as they are the same." [UOC:GVG] parts per hundred parts per thousand "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same." [UOC:GVG] "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]." [UOC:GVG] parts per million parts per billion "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000 regardless of the units of measure as long as they are the same or 1 part in 10^[9]." [UOC:GVG] "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[12]." [UOC:GVG] parts per trillion "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[15]." [UOC:GVG] parts per quadrillion "A mass unit density which is equal to mass of an object in grams divided by the volume in milliliter." [UOC:GVG] gram per milliliter kilogram per liter "A mass unit density which is equal to mass of an object in kilograms divided by the volume in liters." [UOC:GVG] A mass unit density which is equal to mass of an object in grams divided by the volume in liters. gram per litre "A mass unit density which is equal to mass of an object in grams divided by the volume in liters." [UOC:GVG] gram per liter g/L A mass unit density which is equal to mass of an object in grams divided by the volume in liters. UOC:GVG "A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters." [UOC:GVG] milligram per milliliter unit per milliliter "A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one milliliter." [Webmd:Webmd] unit per liter "A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one liter." [UOC:GVG] "A concentration unit which is a standard measure of the mass of a substance in a given volume (density)." [Wikipedia:Wikipedia] mass per unit volume enzyme unit "A catalytic unit activity which is equal to the amount of the enzyme that catalyzes the conversion of 1 micro mole of substrate per minute." [Wikipedia:Wikipedia] "An area density unit which is equal to the mass of an object in kilograms divided by one meter." [NIST:NIST] kilogram per meter "A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad." [Wikipedia:Wikipedia] degree "A dimensionless unit which denoted an irrational real number, approximately equal to 3.14159 which is the ratio of a circle's circumference to its diameter in Euclidean geometry." [Wikipedia:Wikipedia] pi "A dimensionless count unit which denotes the number of molecules." [MGED:MGED] molecule count "A dimensionless percent unit which denotes the homogeneity of a biomaterial." [MGED:MGED] purity percentage "A dimensionless percent unit which denotes the density of an attached or monolayer culture (e.g., cell culture)." [MGED:MGED] confluence percentage A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. "A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius." [Wikipedia:Wikipedia] F degree Fahrenheit A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. Wikipedia:Wikipedia pH A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). "A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+)." [Wikipedia:Wikipedia] A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). Wikipedia:Wikipedia "A specific volume unit which is equal to one liter volume occupied by one kilogram of a particular substance." [NIST:NIST] liter per kilogram milliliter per kilogram "A specific volume unit which is equal to a thousandth of a liter per kilogram or 10^[-3] l/kg." [NIST:NIST] microliter per kilogram "A specific volume unit which is equal to one millionth of a liter per kilogram or 10^[-6] l/kg." [NIST:NIST] "A unit of cell concentration which is equal to one cell in a volume of 1 milliliter." [Bioedonline:Bioedonline] cells per milliliter "A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one cubic meter." [NIST:NIST] katal per cubic meter "A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one thousandth of a cubic meter." [NIST:NIST] katal per liter "A volume per unit volume unit which is equal to one millionth of a liter of solute in one cubic meter of solution." [NIST:NIST] milliliter per cubic meter milliliter per liter "A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution." [NIST:NIST] "A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters." [UOC:GVG] gram per deciliter deciliter "A volume unit which is equal to one tenth of a liter or 10^[-1] L." [NIST:NIST] colony forming unit "A dimensionless count unit which a measure of viable bacterial numbers." [Wikipedia:Wikipedia] plaque forming unit "A dimensionless count unit which a measure of plague forming units in a given volume." [Wikipedia:Wikipedia] colony forming unit per volume "A concentration unit which a measure of viable bacterial numbers in a given volume." [Wikipedia:Wikipedia] colony forming unit per milliliter "A colony forming unit which a measure of viable bacterial numbers in one milliliter." [Wikipedia:Wikipedia] plaque forming unit per milliliter "A concentration unit which a measure of plague forming units in one milliliter." [UOC:GVG] disintegrations per second "An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per second or there is one atom disintegration per second." [ORCBS:ORCBS] "An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy." [Wikipedia:Wikipedia] volt "An electrical charge unit which is equal to the amount of charge transferred by a current of 1 ampere in 1 second." [WordNet:WordNet] coulomb dalton "An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state." [Wikipedia:Wikipedia] kilodalton "A mass unit which is equal to one thousand daltons." [Wikipedia:Wikipedia] "An energy unit which is equal to the amount of electrical energy equivalent to a one-watt load drawing power for one hour." [Wikipedia:Wikipedia] watt-hour "An energy unit which is equal to 1,000 watt-hours." [Wikipedia:Wikipedia] kilowatt-hour weber "A magnetic flux unit which is equal to the amount of flux that when linked with a single turn of wire for an interval of one second will induce an electromotive force of one volt." [ScienceLobby:ScienceLobby] tesla "A magnetic flux density unit which is equal to one weber per square meter." [WordNet:WordNet] volt-hour "A magnetic flux unit which is equal to 3600 Wb." [UOC:GVG] kilovolt-hour "A magnetic flux unit which is equal to one thousand volt-hours." [UOC:GVG] "An information unit which refers to a digit in the binary numeral system, which consists of base 2 digits (ie there are only 2 possible values: 0 or 1)." [Wikipedia:Wikipedia] bit "An information unit which is equal to 8 bits." [Wikipedia:Wikipedia] byte "An information unit which is equal to 1000 bytes." [Wikipedia:Wikipedia] kilobyte megabyte "An information unit which is equal to 1000 kB." [Wikipedia:Wikipedia] "An image resolution unit which is a standard measure of the amount of spatial detail in an image." [Wikipedia:Wikipedia] chroma sampling unit "An image resolution unit which is a standard measure of the amount of contrast available in a pixel." [Wikipedia:Wikipedia] dynamic range unit dots per inch "A spatial resolution unit which is a standard measure of the printing resolution, in particular the number of individual dots of ink a printer or toner can produce within a linear one-inch space." [Wikipedia:Wikipedia] "A spatial resolution unit which is equal to a pixel size of one micrometer." [Wikipedia:Wikipedia] micron pixel pixels per inch "A spatial resolution unit which is a standard measure of the resolution of a computer display, related to the size of the display in inches and the total number of pixels in the horizontal and vertical directions." [Wikipedia:Wikipedia] "A spatial resolution unit which is a standard measure of the number of pixels in one millimeter length or width of a digital image divided by the physical length or width of a printed image." [Wikipedia:Wikipedia] pixels per millimeter "A count unit which contains one nucleotide." [UO:GVG] base pair kibibyte "An information unit which is equal to 1024 B." [NIST:NIST] "An information unit which is equal to 1024 KiB." [NIST:NIST] mebibyte millivolt "An electric potential difference unit which is equal to one thousandth of a volt or 10^[-3] V." [UOC:GVG] "An electric potential difference unit which is equal to one thousand volts or 10^[3] V." [UOC:GVG] kilovolt microvolt "An electric potential difference unit which is equal to one millionth of a volt or 10^[-6] V." [UOC:GVG] "An electric potential difference unit which is equal to one billionth of a volt or 10^[-12] V." [UOC:GVG] nanovolt "An electric potential difference unit which is equal to one trillionth of a volt or 10^[-12] V." [UOC:GVG] picovolt "An electric potential difference unit which is equal to one million volts or 10^[6] V." [UOC:GVG] megavolt "A surface tension unit which is equal to one newton per meter." [NIST:NIST] newton per meter "A surface tension unit which is equal to one dyne per centimeter." [Wikipedia:Wikipedia] dyne per cm pascal second "A viscosity unit which is equal to one pascale per second." [NIST:NIST] poise "A viscosity unit which is equal to one dyne second per square centimeter." [Wikipedia:Wikipedia] "A ratio unit which is an indicator of sound power per unit area." [techtarget:techtarget] decibel "A unit which is a standard measure of the estimate of the stochastic effect that a non-uniform radiation dose has on a human." [Wikipedia:Wikipedia] effective dose unit "An electrical conduction unit which is equal to A/V." [NIST:NIST] siemens "An heat conduction unit which is equal to one watt divided by meter kelvin." [NIST:NIST] watt per meter kelvin "A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J." [Wikipedia:Wikipedia] electronvolt volt per meter "The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field] absorbance unit "A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light." [Wikipedia:http\://en.wikipedia.org/wiki/Absorbance] microliters per minute A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. "A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute." [UOC:GVG] uL/min microlitres per minute A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. UOC:GVG "A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth." [url:en.wiktionary.org/wiki/mmHg] millimetres of mercury "A mass unit density which is equal to mass of an object in milligrams divided by the volume in liters." [UOC:GVG] milligram per liter "A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters." [UOC:GVG] microgram per milliliter nanogram per milliliter "A mass unit density which is equal to mass of an object in nanograms divided by the volume in milliliters." [UOC:GVG] "A unit per milliliter unit which is equal to one thousandth of a unit of an agreed arbitrary amount per one milliliter." [UOC:GVG] milliunits per milliliter "A rate unit which is equal to one over one nanomolar second." [UOC:GVG] count per nanomolar second "A rate unit which is equal to one over one molar second." [UOC:GVG] count per molar second kilogram per hectare "An area density unit which is equal to the mass of an object in kilograms divided by the surface area in hectares." [UO:GVG] "A rate unit which is equal to one over one nanomolar." [UO:GVG] count per nanomolar count per molar "A rate unit which is equal to one over one molar." [UO:GVG] "A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters." [UOC:GVG] microgram per liter "A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per kilogram body weight of the recipient subject." [UO:PC] milligram per kilogram milligram per square meter "A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per square meter of surface area of the recipient subject." [UO:PC] "A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered over time to a recipient subject, expressed in terms of the size of the subject." [UO:PC] dosage unit milligram per kilogram per day "A dosage unit which is equal to 1 milligram per day of a toxic or pharmaceutical substance per kilogram body weight of the recipient subject." [UO:PC] relative light unit "A derived unit which is a measure of relative light intensity, as typically measured by a luminometer, spectrophotometer, or fluorimeter in biological research applications." [UO:PC] "A relative light unit which is a measure of relative luminescence intensity." [UO:PC] relative luminescence unit relative fluorescence unit "A relative light unit which is a measure of relative fluorescence intensity." [UO:PC] megaHertz "A frequency unit which is equal to one million hertz or 10^[6] V." [UOC:GVG] "A unit used to express distances on a genetic map. In genetic mapping, distances between markers are determined by measuring the rate of meoitic recombination between them, which increases proportionately with the distance separating them. A cM is defined as the length of an interval in which there is a 1% probability of recombination. On the average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA, although this can vary widely due to hot and cold spots of recombination." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html] centiMorgan centiRay "A unit of genetic map distance defined corresponding to an interval in which there is a 1% probability of X-irradiation induced breakage. To be completely specified, the unit must be qualified by the radiation in dosage in rads (e.g. cR8000), because this determines the actual breakage probability." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html] megabasepair "A unit equal to one million base pairs" [UOC:GVG] "A unit equal to one billion base pairs." [UOC:GVG] gigabasepair square micrometer "An area unit which is equal to an area enclosed by a square with sides each 1 micrometer long." [NIST:NIST] millisiemens "An electrical conduction unit which is equal to one thousandth of a siemen or 10^[-3] siemens." [NIST:NIST] micromole per litre "A specific concentration unit which is equal to 1 micromole in a given volume of one thousandth of a cubic meter." [NIST:NIST] micromole per kilogram "A specific concentration unit which is equal to 1 micromole of a given substance per kilogram of solvent." [UOB:LKSR] millimeters per day "A speed/velocity unit which is equal to the speed of an object traveling 1 millimeter distance in one day." [UOB:LKSR] "A speed/velocity unit which is equal to the speed of an object traveling 1 kilometer distance in one hour." [NIST:NIST] kilometer per hour "A mass unit which is equal to 1/12 the mass of 12C" [Wikipedia:Wikipedia] milli hectare "An area unit which is equal to an area of 10,000 square meters. Equivalent to 2.471 acres." [Wikipedia:Wikipedia] "A length unit which is equal to 0.0254 metres." [Wikipedia:Wikpiedia] inch thou "A length unit which is equal to 0.0254 millimetres." [Wikipedia:Wikpiedia] "A length unit which is equal to 0.3048 metres, or 12 inches." [Wikipedia:Wikpiedia] foot yard "A length unit which is equal to 0.9144 metres, or 3 feet." [Wikipedia:Wikpiedia] "A length unit which is equal to 20.1168 metres, 66 feet, or 22 yards." [Wikipedia:Wikpiedia] chain "A length unit which is equal to 20,116.8 metres, 660 feet, or 10 chains." [Wikipedia:Wikpiedia] furlong "A length unit which is equal to 1,609.344 metres, or 8 furlongs." [Wikipedia:Wikpiedia] mile league "A length unit which is equal to 3 miles, or 4,828.032 metres" [Wikipedia:Wikpiedia] maritime length unit "A maritime length unit is one used primarily at sea." [Wikipedia:Wikpiedia] "A maritime length unit which is equal to 6.08 feet, or 1.853184 metres" [Wikipedia:Wikpiedia] fathom "A maritime length unit which is equal to 608 feet, 100 fathoms, or 185.3184 metres" [Wikipedia:Wikpiedia] cable "A maritime length unit which is equal to 6,080 feet, 10 cables, or 1,853.184 metres" [Wikipedia:Wikpiedia] nautical mile perch "An area unit which is equal to an area of 25.292,852,64 square meters, or 1 square rod." [Wikipedia:Wikipedia] "An area unit which is equivalent to 1 furlong x 1 rod. This is equal to an area of 1,011.714,1056 square meters, or 40 square rods." [Wikipedia:Wikipedia] rood acre "An area unit which is equivalent to 1 furlong x 1 chain. This is equal to an area of 4,046.856,4224 square meters, or 43,500 square feet." [Wikipedia:Wikipedia] fluid ounce "An imperial volume unit which is equivalent to 28.413,0625 millilitres." [Wikipedia:Wikipedia] gill "An imperial volume unit which is equivalent to 142.065,3125 millilitres." [Wikipedia:Wikipedia] pint "An imperial volume unit which is equivalent to 568.261,25 millilitres." [Wikipedia:Wikipedia] quart "An imperial volume unit which is equivalent to 1,136.5225 millilitres, or two pints." [Wikipedia:Wikipedia] gallon "An imperial volume unit which is equivalent to 4,546.09 millilitres, or 8 pints." [Wikipedia:Wikipedia] "An imperial mass unit which is equivalent to 64.798,91 milligrams." [Wikipedia:Wikipedia] grain drachm "An imperial mass unit which is equivalent to 1.771,845,195,3125 grams, or 1/256 of 1 pound." [Wikipedia:Wikipedia] "An imperial mass unit which is equivalent to 28.349,523,125 grams, or 1/16 of 1 pound." [Wikipedia:Wikipedia] ounce pound "An imperial mass unit which is equivalent to 453.592,37 grams." [Wikipedia:Wikipedia] stone "An imperial mass unit which is equivalent to 6,350.293,18 grams, or 14 pounds." [Wikipedia:Wikipedia] "An imperial mass unit which is equivalent to 12.700,586,36 kilograms, or 28 pounds." [Wikipedia:Wikipedia] quarter hundredweight "An imperial mass unit which is equivalent to 50.802,345,44 kilograms, 112 pounds, or 8 stone." [Wikipedia:Wikipedia] "An imperial mass unit which is equivalent to 1,016.046,9088 kilograms, or 2,240 pounds." [Wikipedia:Wikipedia] ton slug "An imperial gravitational unit which is equivalent to a mass that accelerates by 1ft/s² when a force of one pound (lbf) is exerted on it." [Wikipedia:Wikipedia] "A metric teaspoon is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions. It equals a 5mL volume." [Wikipedia:https://en.wikipedia.org/wiki/Teaspoon] teaspoon micromole "A substance unit which is equal to one millionth of a mole." [UOB:LTS] gram per square meter "An area density unit which is equal to the mass of an object in grams divided by the surface area in meters squared." [NIST:NIST] true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg true GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z contrib to MF GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP From ligand activity to has_ligand This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction From has_ligand to ligand activity effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).