Product version Yu Lin (YL) Arzucan Ozgur Junguk Hur Yongqun "Oliver" He (YH) Zuoshuang "Allen" Xiang 2022-03-27 he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles. OWL-DL An ontology of interactions and interaction networks INO: Interaction Network Ontology 1.1.13 Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note imported from expand expression to OBO foundry unique label elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) an annotation property that lists keyword(s) useful for literature tagging and retrieval of sentences containing the type (or kind) of entity (e.g., interaction) as shown by the ontology term label and definition. Yongqun He has literature mining keywords literature mining example Yongqun He an example of usage for literature mining example of literature mining keyword usage an annotation property that specifies the dependency pattern of the literature keywords that match to the ontology interaction type. Arzucan Ozgur, Junguk Hur, Yongqun He has keyword dependency pattern An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation https://oborel.github.io/obo-relations/temporal-semantics/ An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property logical macro assertion on an annotation property relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' Chris Mungall is direct form of relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y Chris Mungall is indirect form of Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" cjm 2018-03-13T23:59:29Z is directional form of cjm 2018-03-14T00:03:16Z is positive form of cjm 2018-03-14T00:03:24Z is negative form of part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. cjm 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy has_rank Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. An entity responsible for making contributions to the content of the resource. Contributor Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges. The extent or scope of the content of the resource. Coverage Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. An entity primarily responsible for making the content of the resource. Creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). The physical or digital manifestation of the resource. Format Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN). An unambiguous reference to the resource within a given context. Resource Identifier Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom. A language of the intellectual content of the resource. Language Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity. An entity responsible for making the resource available Publisher Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a related resource. Relation Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource. Information about rights held in and over the resource. Rights Management The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Title Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element. The nature or genre of the content of the resource. Resource Type has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym in_subset label 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of 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 an object property between an activation process and a material entity that acts as an activator during the process. Yongqun He has activator has_controller controls has_next_step lacks part David Osumi-Sutherland <= Primitive instance level timing relation between events before or simultaneous with David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with David Osumi-Sutherland t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) before 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 di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 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. encompasses 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 Previously had ID http://purl.obolibrary.org/obo/RO_0002123 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 starts David Osumi-Sutherland starts before David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes David Osumi-Sutherland io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland d during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during 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 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 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to inverse of starts with Chris Mungall Allen starts Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. 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 started by starts with 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 p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. Chris Mungall produces has output 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 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 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 inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q Chris Mungall directly positively regulates directly activates (process to process) directly activates p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one. Chris Mungall indirectly positively regulates indirectly activates Chris Mungall directly negatively regulates directly inhibits (process to process) directly inhibits Chris Mungall indirectly negatively regulates indirectly inhibits 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 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 p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall directly provides input for (process to process) directly provides input for transitive form of directly_provides_input_for Chris Mungall This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for') transitively provides input for (process to process) transitively provides input for 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 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 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 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 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 coefficient tells us how many molecules of a given formula are present. For example, 2 H2O means we have 2 molecules of water. An data property that represents the coefficient value in a chemical reaction equation. Specifically, the cofficent is the number in front of a formula in a chemical equation. YH has coefficient BFO:0000001 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 BFO:0000002 continuant Continuant 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 BFO:0000003 occurrent Occurrent 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 BFO:0000004 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 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 BFO:0000008 t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region BFO:0000015 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. 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 BFO:0000016 disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition BFO:0000017 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 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 BFO:0000019 quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality BFO:0000020 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 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 BFO:0000023 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 BFO:0000029 site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site BFO:0000030 object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object BFO:0000031 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. 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 BFO:0000034 function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function BFO:0000038 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region BFO:0000040 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. 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 BFO:0000141 immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity BFO:0000148 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. CHEBI:13302 CHEBI:21123 CHEBI:33698 CHEBI:4291 CAS:9007-49-2 KEGG:C00039 Deoxyribonucleic acid deoxyribonucleic acids chebi_ontology (Deoxyribonucleotide)m (Deoxyribonucleotide)n (Deoxyribonucleotide)n+m DNA DNAn DNAn+1 DNS Desoxyribonukleinsaeure deoxyribonucleic acids desoxyribose nucleic acid thymus nucleic acid CHEBI:16991 deoxyribonucleic acid CHEBI:16991 Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity CHEBI:23367 A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. nucleic acids chebi_ontology NA Nukleinsaeure Nukleinsaeuren acide nucleique acides nucleiques acido nucleico acidos nucleicos CHEBI:33696 nucleic acid CHEBI:33696 High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. CAS:63231-63-0 ribonucleic acid ribonucleic acids chebi_ontology RNA RNS Ribonukleinsaeure pentosenucleic acids ribonucleic acids ribose nucleic acid yeast nucleic acid CHEBI:33697 ribonucleic acid CHEBI:33697 CL:0000000 A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FMA:68646 GO:0005623 KUPO:0000002 VHOG:0001533 WBbt:0004017 XAO:0003012 cell The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell CL:0000066 A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. BTO:0000414 CALOHA:TS-2026 CARO:0000077 FBbt:00000124 FMA:66768 WBbt:0003672 epitheliocyte cell epithelial cell CL:0000235 A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. BTO:0000801 CALOHA:TS-0587 FMA:63261 FMA:83585 histiocyte cell Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid. macrophage GO:0006461 The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. protein amino acid acetylation biological_process GO:0006473 protein acetylation GO:0006473 A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. apoptotic cell death apoptotic programmed cell death programmed cell death by apoptosis activation of apoptosis apoptosis apoptosis signaling apoptotic program type I programmed cell death biological_process GO:0006915 apoptotic process GO:0006915 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. biological process physiological process biological_process GO:0008150 biological_process GO:0008150 Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538). biological_process GO:0008219 cell death GO:0008219 A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. caspase-independent cell death non-apoptotic programmed cell death nonapoptotic programmed cell death biological_process GO:0012501 programmed cell death GO:0012501 The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. biological_process GO:0016310 phosphorylation GO:0016310 The covalent attachment of a myristoyl group to a protein. protein amino acid myristoylation biological_process GO:0018377 protein myristoylation GO:0018377 The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer. protein oligomer assembly protein oligomer formation protein oligomerization biological_process GO:0051259 protein complex oligomerization GO:0051259 IAO:0000027 data item Data items include counts of things, analyte concentrations, and statistical summaries. 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 IAO:0000030 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 IDO:0000405 A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition. Albert Goldfain Alexander Diehl Lindsay Cowell Clostridium botulinum is an example of an entity with the capability to bear the pathogen role but that does not have the capability to bear the infectious agent role or the parasite role. The influenza viruses are examples of organisms that can bear both the infectious agent and pathogen roles. pathogen role IDO:0000528 A material entity with a pathogenic disposition. Albert Goldfain Alexander Diehl Lindsay Cowell pathogen IDO:0000629 A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism. Albert Goldfain Alexander Diehl Lindsay Cowell host role INO:0000001 Interaction network is a process that includes a network of at least two interactions. If the interaction is physical and molecular, the interaction network is molecular interactions usually found in cells. YH, ZX http://en.wikipedia.org/wiki/Interaction_network interaction network INO:0000002 Interaction is a processual entity that has two or more participants (i.e., interactors) that have an effect upon one another. YH, ZX interact, interacted, interacting, interaction, interaction, interactor, interactors, interacts, participates; plays a role, contribute, contributed, contributes, contributing, engagement, engagements, engages, engaging, involve, involved, involves, involving, act, acted, acting, acts interaction INO:0000003 an interaction network that includes at least two interactions and has a start point(s) and an end point(s). YH, ZX pathway INO:0000004 an interaction network model that is represented by a probabilistic graphical model (a type of statistical model) that represents a set of random variables and their conditional dependencies via a directed acyclic graph (DAG). YH, ZX WEB: http://en.wikipedia.org/wiki/Bayesian_network Bayesian network INO:0000005 an regulator role that is borne by a material entity that regulates an interaction. YH regulator role INO:0000007 a positive regulation that one interactor up-regulates another. YH up-regulate, up-regulations, up-regulated, up-regulating, upregulate, upregulations, upregulated, upregulating up-regulation INO:0000008 an interactor that regulates an interaction. YH interaction regulator INO:0000009 an interactor role that is borne by a material entity that acts as an input of an interaction. YH, ZX interaction input role input interactor role INO:0000010 an interactor role that is borne by a material entity that acts as an output of an interaction. YH, ZX interaction output role output interactor role INO:0000011 a positive regulator role that is borne by a material entity that activates an interaction. YH activator role INO:0000012 an interaction network model that is represented by at least two mutual information interactions. YH, ZX WEB: http://en.wikipedia.org/wiki/Mutual_information mutual information network INO:0000013 a node is an object that represents an interactor in a graph of an interaction or interaction network. YH, ZX is node equal to interactor?? (YL) node INO:0000014 an edge is an object that represents a graphic line that links two interactors in an interaction. YH, ZX edge INO:0000015 a role that is borne by a material entity to act as a participant in an interaction process. YH, ZX interactor role INO:0000016 an interactor is a material entity that participates in an interaction. YL. YH. ZX. interactor INO:0000017 a positive interaction regulator that activates an interaction. YH activator INO:0000018 a biological interaction that occurs in the organism level. Examples: a bacterium interacts with a mouse, a cat interacts with a dog YL.YH. ZX. organism-organism interaction INO:0000019 A two-way interaction is an interaction that includes two different directions among two interactors. YH two-way interaction INO:0000021 a pathway that exists in human body. YH, ZX human molecular pathway INO:0000022 an up-regulation that one interactor up-regulates the secretion of another interactor. YH up-regulate, up-regulations, up-regulated, up-regulating, upregulate, upregulations, upregulated, upregulating up-regulation of secretion INO:0000023 an interaction involving human molecules YH, ZX YH: This branch may be made obsolete since we now have human INO (HINO). human molecular interaction INO:0000024 a positive regulation that one interactor activates another. YH, ZX activate, activated, activates, activating, activation, activator, activators, activity activation INO:0000025 an interaction that includes a gene and a cell as interactors. YL.YH. ZX. gene-cell interaction INO:0000026 an activation process where one protein is activated by a material entity YH protein activation, protein activated, activates protein, activating protein, activated protein YH: in literature mining, the protein can be any specific protein symbol or protein name. protein activation INO:0000027 a biological interaction that involves two cells as interactors. YL.YH. ZX. cell-cell interaction INO:0000028 an activation process where one protein is activated by a gene mutant YH protein activation by gene mutant protein activation by mutant, protein activated by mutant, mutant activates protein, activating protein by mutant, mutant activated protein YH: in literature mining, the protein can be any specific protein symbol or protein name. In addition, the mutant can be a mutant of any gene and the name of the mutant can be any specific name given by the research who generated the mutant. protein activation by mutant INO:0000029 a biochemical binding where a substance binds to the same site an agonist would bind to without causing activation of the receptor YH, ZX WEB: http://en.wikipedia.org/wiki/Receptor_antagonist antagonise, antagonised, antagonises, antagonising, antagonist, antagonists, antagonize, antagonized, antagonizes, antagonizing antagonism INO:0000030 an interaction that involves a gene and its environment (e.g., calcium in blood). YL.YH. ZX. gene-enviroment interaction INO:0000031 a regulation process that regulates the location of a protein YH, AO location // (protein) // dependent, location // (protein) // depends "Localization of SpoIIE was shown to be dependent on the essential cell division protein FtsZ" (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10747015) regulation of protein location INO:0000032 a gene expression regulation process that involves the regulation of a gene transcription. YH, AO, JH regulation of gene transcription transcribed, transcribed by, regulates the transcription of, regulated the transcription of, regulates // transcription, regulated // transcription, under the control of // transcription, essential for // transcription, trascription depends, transcription // dependent, control // transcription, controlling // transcription, requires // transcription amod(transcription, controlling), amod(transcription, dependent), amod(expression, dependent), nsubj(dependent, transcription), nsubj(control, expression), nmod:for(regulator, transcription), nmod:of(activator, transcription), nsubjpass(recognized, promoter) regulation of transcription INO:0000033 a negative regulation that attenuates the virulence of a pathogenic microbe. YH, ZX attenuate, attenuated, attenuates, attenuating attenuation INO:0000034 a gene expression regulation process that involves the regulation of a protein translation process. YH, AO regulation of gene translation regulation of protein translation translation depends, translation // dependent, regulates // translation, regulated // translation, regulates the translation of, regulated the translation of, regulation // production, regulated // production, regulate // production "Transcription of ydhD was dependent on SigE" (Reference: http://www.ncbi.nlm.nih.gov/pubmed/11011148) regulation of translation INO:0000035 a phosphorylation process that adds a phosphate to a protein kinase (possibly affecting its activity) by virtue of its own enzymic activity. YH, ZX autophosphorylate, autophosphorylated, autophosphorylates, autophosphorylating, autophosphorylation autophosphorylation INO:0000037 a regulation process that regulates the activation of a gene so that the gene is expressed at a particular time YH, AR, JH WEB: http://www.medilexicon.com/medicaldictionary.php?t=970 essential for // activation, essential for // activation, activated // expression, activates // expression, control // activation, controlling // activation, requires // activation, requiredd // activation "sequestration of SpoIIE protein into the prespore plays an important role in the control of sigmaF activation and in coupling this activation to septation." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10476035) regulation of gene activation INO:0000038 a regulation process that positively regulates gene expression level YH, AR positive regulation // expression, increase // expression, induced // dependent, induced // via, induced // by, induced // dependent // presence "YtxH and YvyD seemed to be induced after phosphate starvation in the wild type in a sigma(B)-dependent manner." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10913081) positive regulation of gene expression INO:0000039 a regulation process that negatively regulates gene expression level YH, AR essential for // negative regulation, negatively regulated // expression, negatively regulates // expression, negative regulator // transcription "These results suggest that YfhP may act as a negative regulator for the transcription of yfhQ, yfhR, sspE and yfhP." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10463184) negative regulation of gene expression INO:0000040 a human molecular reaction that is specifically a biochemical reaction YH. ZX human biochemical reaction INO:0000041 place holder for physical entities Obsolete note: This class is replaced by CHEBI term: molecular entity physical entity - obsolete INO:0000042 a negative regulation process that down-regulates gene expression level YH, AO negatively regulated // transcription, negatively regulates // transcription, negatively controls // transcription, negatively controled // transcription dobj(preventing,transcription) negative regulation of gene transcription INO:0000043 a negative regulation process that down-regulates protein translation level YH, AO negatively regulated // translation, negatively regulates // translation, limits // production, limited // production negative regulation of protein translation INO:0000044 a regulation process that regulates gene expression level YH, AO, JH regulation of gene expression regulated // expression, regulates // expression, essential // expression, control // expression, controlled // expression, controlling // expression, controls // expression, expression under control, essential for // expression, responsible for production, essential for production, regulates the production of, regulated the production of, responsible // production, responsible // production, affect // production, affected // production, depend // expression, dependent // expression, level // (gene) // dependent, requires // expression, required // expression, regulated by // pathway // relying on, regulon // includes, member of // regulon "SigK and GerE were essential for ykvP expression" (Reference: http://www.ncbi.nlm.nih.gov/pubmed/11011148) amod(expression, dependent) gene expression regulation INO:0000045 a gene expression process that results in protein production from a gene DNA sequence. YH, ZX gene translation WEB: http://en.wikipedia.org/wiki/Translation_%28biology%29 translation, translated, translating, encoding, encodes, protein production protein translation INO:0000046 a negative regulation of gene transcription process that specifiies the negative regulation being an inhibition. YH, AO inhibited // transcription, inhibits // transcription, repressed // transcription, repress // transcription, prevented // transcription, prevents // transcription, prevent // transcription "GerE protein inhibits transcription in vitro of the sigK gene." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739) inhibition of gene transcription INO:0000047 an interactor that starts or speeds up a chemical reaction while undergoing no permanent change itself. YH chemical reaction catalyst INO:0000048 a coprecipitation that occurs through an immunoprecipitation process. YH, ZX co-immunoprecipitation coimmunoprecipitate, coimmunoprecipitated, coimmunoprecipitates, coimmunoprecipitating, coimmunoprecipitation, coimmunopreticipate, coimmunopreticipated, coimmunopreticipates, coimmunopreticipating, co-immunoprecipitate, co-immunoprecipitated, co-immunoprecipitates, co-immunoprecipitating, co-immunoprecipitation, co-immunopreticipate, co-immunopreticipated, co-immunopreticipates, co-immunopreticipating coimmunoprecipitation INO:0000049 a regulation of transcription process that inviolves a positive regulation. YH, AO positively regulated // transcription, negatively regulates // transcription, stimulating // transcription, stimulates // transcription, stimulated // transcription, induction // transcription, induced // transcription, induces // transcription, inducing // transcription, driven // transcription, drives // transcription dobj(stimulating,transcription) positive regulation of gene transcription INO:0000050 an indirect association that one interactor competes with another interactor in a specfiic process. YH, ZX compete, competed, competes, competing competition INO:0000051 a positive regulation of gene transcription process that inviolves an activation of the gene transcription. YH, AO activated // transcription, activates // transcription "Transcription of the cotB, cotC, and cotX genes by final sigma(K) RNA polymerase is activated by a small, DNA-binding protein called GerE." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10788508) activation of gene transcription INO:0000052 an activation of gene transcription that is achieved by a low level of a protein YH, AO low level // activated // transcription, low level // activates // transcription, low concentration // activated // transcription "A low level of GerE activated transcription of cotD by sigmaK." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739) activation of gene transcription by low level protein INO:0000053 a regulation of translation process that positively regulates protein translation level YH, AO positively regulated // translation, positively regulates // translation, increases // production, increased // production, increasing // production, increasing // production "ComK ... thereby increasing the production of the FlgM." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/9696775) positive regulation of protein translation INO:0000054 a direct interaction where an antigen interacts with an antibody physically. YH WEB: http://en.wikipedia.org/wiki/Antigen-antibody_interaction antigen-antibody interaction INO:0000055 a regulation process that regulates an activity of a protein YH, AO protein activity regulation regulated // activity, regulates // activity, essential // activity, controlled // activity, controls // activity, activity under control, essential for // activity If you can detect your protein on a western blot, and it is migrating to the apparent molecular weight that you expect, you can say for definite that the protein is being expressed. This means that the primary structure (i.e. the amino acid chain) has been synthesised. Activity depends on, for example, correct folding of the enzyme, the presence of any required cofactors, proper targetting (e.g. if its a membrane protein) and that there are mutations crucial catalytic residues. Western blotting tells you nothing about these things. (Reference: http://www.protocol-online.org/biology-forums/posts/30248.html) regulation of protein activity INO:0000056 a gene expression that has decreased volume. YH, ZX decreased gene expression downexpression INO:0000057 a regulation that one interactor controls the quality of another interactor to a specific range YH, ZX control, controled, controling, controlled, controlling, controls controling INO:0000058 a direct physical association that one interactor is converted from another interactor. YH, ZX conversion, convert, converted, converting, converts, derived, derives, derivation conversion INO:0000059 an indirect association that one interactor cooperates with another interactor in a specfiic process. YH, ZX cooperate, cooperated, cooperates, cooperating cooperation INO:0000060 a colocalization that two interactors are precipitated together. YH, ZX co-precipitation coprecipitate, coprecipitated, coprecipitates, coprecipitating, coprecipitation, copreticipate, copreticipated, copreticipates, copreticipating, co-precipitate, co-precipitated, co-precipitates, co-precipitating, co-precipitation, co-preticipate, co-preticipated, co-preticipates, co-preticipating coprecipitation INO:0000061 an indirect association that two interactors are correlated in a process without defined influence of each other. YH, ZX correlate, correlated, correlating correlation INO:0000062 Example: A and B costimulate C. The relations between A and C or between B and C are regulation. However, the relation between A and B is an association. YH, ZX, AO costimulate, costimulated, costimulating costimulation INO:0000063 an interaction that involves a cell and its environment as interactors YH cell-environment interaction INO:0000064 an immuno-precipitation that one interactor is precipitated based on an cross- immunological precipitation process. YH, ZX cross-immunoprecipitate, cross-immunoprecipitated, cross-immunoprecipitates, cross-immunoprecipitating, cross-immunoprecipitation, crossimmunoprecipitate, crossimmunoprecipitated, crossimmunoprecipitates, crossimmunoprecipitating, crossimmunoprecipitation cross-immunoprecipitation interaction INO:0000065 an interaction that involves an organism and its environment as interactors YH organism-environment interaction INO:0000066 YH, ZX an antigen-antibody interaction where an antibody interats with an antigen that differs from the immunogen used to generate antibody. immunological cross-reaction INO:0000067 a regulation of protein activitiy process that involves a negative regulation YH, AO negative protein activity regulation negatively regulated // activity, negatively regulates // activity negative regulation of protein activity INO:0000068 a regulation in which one interactor has a negative effect on another interactor YH: different types of negative regulations exist. These types are related to different qualities and phenotyes of regulated targets. YH, ZX down-regulate, down-regulations, down-regulated, down-regulating, downregulate, downregulations, downregulated, downregulating negative regulation INO:0000069 an interactor role that is played by a material entity that starts or speeds up a chemical reaction while undergoing no permanent change itself. YH chemical reaction catalyst role INO:0000070 a negative regulation of protein activitiy process that involves an inhibition of a protein activity YH, AO inhibited // activity, inhibites // activity, inhibition // activity "... FlgM antisigma factor that inhibits sigmaD activity." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/9696775) inhibition of protein activity INO:0000071 a regulation of transcription process that occurs through the binding to a promotor of a gene YH, AO binds // promoter, bound to // promoter, binding // promoter, recognize // promoter, recognized // promoter, expressed // promoter, dependent // promoter. depdenent // promoter of (or proceding, procedes), repress // promoter, activate // promoter, regulate // promoter, regulated // promoter, stimulate // promoter, stimulate // transcription // promoter, induced // promoter "We show that GerE binds to two sites that span the -35 region of the cotD promoter." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739) Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the genes that they regulate. Depending on the transcription factor, the transcription of the adjacent gene is either up- or down-regulated. (Ref: https://en.wikipedia.org/wiki/Transcription_factor). regulation of transcription by binding to promoter INO:0000072 a regulation of transcription by binding to promoter that is further classified as a positive regulation YH, AO induce // expression // promoter, induced // transcription // promoter, stimulate // promoter, stimulate // transcription // promoter, induced // promoter, activated // transcription // promoter, activated // promoter, dependent // promoter // drives // expression, dependent // promoter // responsible // transcription, expressed // controlled // promoter "We show that GerE binds to two sites that span the -35 region of the cotD promoter." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739) Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the genes that they regulate. Depending on the transcription factor, the transcription of the adjacent gene is either up- or down-regulated. (Ref: https://en.wikipedia.org/wiki/Transcription_factor). positive regulation of transcription by binding to promoter INO:0000073 a negative regulation that results in the decrease of one interactor volume. YH, ZX reduction decrease, decreased, decreases, decreasing, decreasing, reduce, reduced, reduces, reducing, diminish, diminished, diminishes, diminishing, declining, declines, declination, limit, limited, limiting, limits decrease INO:0000074 a regulation of transcription by binding to promoter that is further classified as a positive regulation YH, AO negatively regulate // promoter, negatively regulated // promoter, repressed // promoter, represses // promoter, repress // promoter, binds // transcriptional start site // repressor, bound // transcriptional start site // repressor "We show that GerE binds to two sites that span the -35 region of the cotD promoter." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739) Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the genes that they regulate. Depending on the transcription factor, the transcription of the adjacent gene is either up- or down-regulated. (Ref: https://en.wikipedia.org/wiki/Transcription_factor). negative regulation of transcription by binding to promoter INO:0000075 a positive regulation of gene expression process that activates a gene so that the gene is expressed at a particular time YH, AR, JH WEB: http://www.medilexicon.com/medicaldictionary.php?t=970 activation // (gene), activated // (gene), activates // // (gene), activated // action gene activation INO:0000076 an enzymatic reaction that leads to the breakdown of a biochemical entity. YH, ZX degradation, degradations, degrade, degraded, degrades, degrading biochemical degradation INO:0000077 a regulation of transcription process where two or more regulators regulate a gene transcription YH, AO transcription // combined action, transcription // results from // combined action "In vitro transcription experiments suggest that the differential pattern of cot gene expression results from the combined action of GerE and another transcription factor, SpoIIID." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10788508) co-regulation of transcription INO:0000078 an activation of gene transcription that is achieved by a high level of a protein YH, AO high level // activated // transcription, high level // activate // transcription, high concentration // activated // transcription "A low concentration of GerE activated cotB transcription by final sigma(K) RNA polymerase, whereas a higher concentration was needed to activate transcription of cotX or cotC." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739) activation of gene transcription by high level protein INO:0000079 a regulation of transcription process through binding to a promoter or regulating the promoter binding activity YH, AO recognize // promoter, recognized // promoter, expressed // promoter, dependent // promoter. depdenent // promoter of (or proceding, procedes), repress // promoter, activate // promoter, regulate // promoter, regulated // promoter, stimulate // promoter, stimulate // transcription // promoter, induced // promoter "The -10 and -35 sequences of the sigmaB- and sigmaF-dependent promoters of katX overlap, and the transcriptional start points used by EsigmaB and EsigmaF differ by only one nucleotide." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10503549) Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the genes that they regulate. Depending on the transcription factor, the transcription of the adjacent gene is either up- or down-regulated. (Ref: https://en.wikipedia.org/wiki/Transcription_factor). promoter-based regulation of transcription INO:0000081 an activation of gene transcription that is achieved by a phosphorylated protein YH, AO phosphorylated // activator // transcription, phosphorylated // activates // transcription, phosphorylated // activate // transcription, phosphorylated // activated // transcription "Spo0A, which when phosphorylated is an activator of sigE transcription." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10383978) activation of gene transcription by phosphorylated protein INO:0000083 YH human molecular catalysis INO:0000084 a negative regulation that results in a destabilization. YH, ZX destabilization, destabilize, destabilized, destabilizes, destabilizing destabilization INO:0000085 a negative regulation process that inhibits gene expression level YH inhibits // expression, inhibited // expression, suppressor // expression, suppress // expression, repress // expression, acts // repressor "CtsR protein acts as a global repressor of the clpC operon." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/9852015) gene expression inhibition INO:0000086 a regulation that one interactor has a dominant effect on the quality of another interactor. This differs from the accessory regulation. YH, ZX determine, determined, determines, determining, cause, caused, causes, causing, lead, leading, leads, led, govern, governed, governing, governs dominant regulation INO:0000088 a protein complex assembly that involves two proteins that form a dimer. YH, ZX dimerize, dimerized, dimerizes, dimerizing protein dimerization INO:0000089 a regulation process that involves in two interactors co-regulate a third interactor. YH co-regulation, co-regulated, co-regulate, co-regulating co-regulation INO:0000090 molecular complex INO:0000091 a negative regulation that results in a disruption. YH, ZX disrupt, disrupted, disrupting, disrupts disruption INO:0000092 YH, ZX dissociate, dissociated, dissociating, dissociation dissociation INO:0000093 a negative regulation that one interactor down-regulates another. YH, ZX down-regulate, down-regulated, down-regulates, down-regulating, down-regulation, downregulate, downregulated, downregulates, downregulating, downregulation, downmodulation, depress, depressed, depresses, depressing, suppress, suppressed, suppresses, suppressing, suppression, suppressor, repress, repressed, represses, repressing, repression, repressor, repressors down-regulation INO:0000094 a positive regulation of gene expression process that up-regulates gene expression level YH, AR essential for // up-regulation, up-regulated // expression, up-regulates // expression gene expression up-regulation INO:0000095 a negative regulation process that down-regulates gene expression level YH down-regulated // expression, down-regulates // expression gene expression down-regulation INO:0000096 an induction that leads to the production of an entity YH: For example, "IL-2 and IL-15 induced the production of IL-17 and IFN-γ in a dose dependent manner by PBMCs.” YH induction of the production, induces the production, induced the production induction of production INO:0000097 a negative regulation that one interactor eliminates another. YH, ZX eliminate, eliminated, eliminates, eliminating, abolish, abolished, abolishes, abolishing, abrogation elimination INO:0000098 a cell-cell interaction that the transfers genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells. YH WEB: http://en.wikipedia.org/wiki/Bacterial_conjugation bacterial conjugation INO:0000099 Interaction leading to the formation of hydrogen bond between two molecules YH WEB: http://www.ncbi.nlm.nih.gov/books/NBK22567/ hydrogen binding INO:0000100 a regulation process where one gene product regulates an assembly process which forms an assembly having another gene product. YH, AR, JH regulated // assembly regulation of assembly INO:0000101 a human molecular interaction where one molecule controls another molecule. YH human molecular control interaction INO:0000102 a biological interaction that uses the information from a gene to synthesize a functional gene product. YH, ZX express, expressed, expresses, expressing, expression, expressions gene expression INO:0000103 a positive regulation that one interactor facilitates a phenomenon such as a phenotype. This is an accessory effect not a major one. YH, ZX facilitate, facilitates, facilitating, faciliteted, help, helps, helped accessory regulation INO:0000104 a regulation of protein activitiy process that involves a positive regulation YH, AO negative protein activity regulation positively regulated // activity, positively regulates // activity, dependent // stimulation positive regulation of protein activity INO:0000105 An interaction that involves a host (host organism or host cell) and pathogen organism at a specific condition. YH host-pathogen interaction INO:0000106 a genetic interaction that forms a hybrid gene formed from two previously separate genes. It can occur as the result of a translocation, interstitial deletion, or chromosomal inversion. YH, ZX WEB: http://en.wikipedia.org/wiki/Gene_fusion gene AND (fuse, fused, fuses, fusing) gene fusion INO:0000107 An host-pathogen interaction where the host is a cell. YH host cell-pathogen interaction INO:0000108 The Salmonella invasin SipB induces macrophage apoptosis by binding to caspase-1 an induction that is achieved by binding to a protein induction ... by binding to // induces .. through binding// induced ... by binding to // caused ... by binding to // causes ... through ... binding YH, AO, JH induction by binding to protein INO:0000109 An host cell-pathogen interaction where the host cell is a macrophage. YH macrophage-pathogen interaction INO:0000110 YH human molecular degradation INO:0000111 a protein dimerization where two proteins are different. YH, ZX heterodimerize, heterodimerized, heterodimerizes, heterodimerizing protein heterodimerization INO:0000112 a protein dimerization where two proteins are the same. YH, ZX homodimerize, homodimerized, homodimerizes, homodimerizing protein homodimerization INO:0000113 The Salmonella invasin SipB induces macrophage apoptosis by binding to caspase-1. From: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC26795/ A macrophage-pathogen interaction that involves a macrophage protein and a pathogen protein. YH macrophage-pathogen PPI macrophage-pathogen protein-protein interaction INO:0000114 a gene expression that has increased volume. YH, ZX increased gene expression overexpression hyper-expression, hyperactivate, hyperactivated, hyperactivates, hyperactivation, hyperexpression, overexpression overexpression INO:0000115 YH, ZX hyperphosphorylate, hyperphosphorylated, hyperphosphorylates, hyperphosphorylation hyperphosphorylation INO:0000116 a translocation that one interactor is precipitated based on an immunological precipitation process. YH, ZX immuno-precipitate, immuno-precipitated, immuno-precipitates, immuno-precipitating, immuno-precipitation, immunoprecipitate, immunoprecipitated, immunoprecipitates, immunoprecipitating, immunoprecipitation, immunopreticipate, immunopreticipated, immunopreticipates, immunopreticipating immuno-precipitation INO:0000117 YH: different types of positive regulations exist. These types are related to different qualities and phenotyes of regulated targets. YH, ZX positively regulate, positive regulations, positively regulated, positively regulating, promote, promoted, promotes, promoting positive regulation INO:0000118 A negative regulation that disables, damages, or impairs the functioning of another entity. YH, ZX impair, impaired, impairing, impairs, cripple, crippled, cripples, crippling, sever, severed, severs impairment INO:0000119 a negative regulation that one interactor inactivates another. YH, ZX inactivate, inactivated, inactivates, inactivating, inactivation inactivation INO:0000120 a positive regulation that leads to the increase of a quality of an entity. YH, ZX augmentation elavation enhancement increase, increased, increases, increasing, augment, augmented, augmenting, augments, elavating, elevate, elevated, elevates, elevating, raise, raised, raises, raising, enhance, enhanced, enhances, enhancing, enhancement increase INO:0000121 human molecular synthesis INO:0000122 a positive regulation that leads to the induction of a new interactor due to the presence of another interactor. YH, ZX leading triggering induce, induced, induces, inducing, induction, trigger, triggered, triggering, triggerring, triggers, initiate, initiated, initiates, initiating, stimulate, stimulation, stimulated, stimulating, dependent // inducible induction INO:0000123 human molecular regulatory reaction INO:0000124 a negative regulation that one interactor inhibites another. YH, ZX inhibit, inhibited, inhibiting, inhibition, inhibitor, inhibitors, inhibits, block, blocked, blocking, blocks inhibition INO:0000125 an interactor that is an input of an interaction. YH input interactor INO:0000126 a negative regulation that one interactor interferes a process. YH, ZX interfere, interferes, interfered, interfering, perturb, perturbed, perturbing, perturbs, obstruction interference INO:0000127 YH human molecular modulation INO:0000128 YH human template reaction regulation INO:0000129 An host-pathogen interaction where the host is a gene mutant YH host gene mutant-pathogen interaction INO:0000130 a human molecular interaction where one molecule converts to another molecule. YH human molecular conversion INO:0000131 human molecular template reaction INO:0000132 small molecule INO:0000133 An organism bearing a host role. host INO:0000134 an interactor role that is borne by a material entity that positively regulates an interaction. YH positive regulator role INO:0000135 An data item that indicates the step number of a pathway. Oliver He pathway step INO:0000137 an interactor role that is borne by a material entity that negatively regulates an interaction. YH negative regulator role INO:0000138 The Salmonella invasin SipB induces macrophage apoptosis by binding to caspase-1. From: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC26795/ A macrophage-pathogen protein-protein interaction that induces cell death. YH macrophage-pathogen PPI inducing cell death INO:0000140 a biochemical reaction that one interactor neutrolizes another. YH, ZX neutralise, neutralised, neutralises, neutralising, neutralize, neutralized, neutralizes, neutralizing neutralization INO:0000141 an interaction regulator that positively regulates an interaction. YH positive regulator INO:0000142 an enzymatic reaction where a molecule gains oxygen. YH, ZX oxidate, oxidated, oxidates, oxidating, oxidation, oxidise, oxidised, oxidises, oxidising, oxidize, oxidized, oxidizes, oxidizing oxidation INO:0000143 An host-pathogen interaction where the pathogen is a gene mutant YH host-pathogen mutant interaction INO:0000144 an interaction regulator that negatively regulates an interaction. YH negative regulator INO:0000145 a negative regulator role that is borne by a material entity that deactivates, inhibits, blocks, or disrupts the action of a biological agent (e.g., enzyme). YH deactivator role INO:0000146 An host cell-pathogen interaction where the host is a macrophage cell YH macrophage-pathogen interaction INO:0000147 an input interactor role that is borne by a material entity that motivates a process. Oliver He https://en.wikipedia.org/wiki/Motivation#Herzberg's_two-factor_theory motivator role INO:0000148 an indirect association that one interactor is preceded by another interactor. YH, ZX precede, preceded, precedes, preceding precedence INO:0000149 YH, ZX prevent, prevented, preventing, prevents prevention INO:0000150 an input interactor role that is borne by a material entity (e.g. status, job security, salary and fringe benefits) that do not motivate if present, but, if absent, result in demotivation. Oliver He https://en.wikipedia.org/wiki/Motivation#Herzberg's_two-factor_theory hygiene factor role INO:0000151 an interactor that is an output of an interaction. YH output interactor INO:0000152 An host cell-pathogen interaction where the host is an epithelial cell YH epithelial cell-pathogen interaction INO:0000153 an activation that repeats. YH, ZX reactivate, reactivated, reactivates, reactivating, reactivation reactivation INO:0000155 a positive regulation that leads the recruitment of one interactor from one location to another. YH, ZX recruit, recruite, recruited, recruites, recruiting, recruits recruitment INO:0000156 We show that caspase-2 functions as an initiator caspase during Staphylococcus aureus α-toxin- and Aeromonas aerolysin-mediated apoptosis in epithelial cells. From: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365430/ YH epithelial cell-pathogen PPI epithelial cell-pathogen protein-protein interaction INO:0000157 A regulation represents a regulatory interaction between two interactors. YH, ZX, AO, JH regulate, regulated, regulates, regulating, regulation, regulator, modulate, modulated, modulates, modulating, modulation, mediate, mediated, mediates, mediating, influence, influenced, influences, influencing, affect, affected, affecting, affects, impact, impacted, impacting, impacts, effect, effected, effecting, effects, require, required, requires, requiring, respond, responded, responding, responds, responsive, change, changed, changes, changing, alter, altered, altering, alters, modified, modifies, modify, modifying, depend, depended, depending, depends, direct, directed, directing, directs, drive, driven, drives, driving, cause, caused, causes, causing, lead, leading, leads, led, target, targeted, targeting, targets, dependent, essential for regulation GO: GO_0065007 INO:0000158 An information content entity that models interaction network Oliver He https://en.wikipedia.org/wiki/Interactome interaction network model INO:0000159 obsolete class INO:0000165 a postive interaction that one interactor increases the stability of another interactor. YH, ZX stabilization, stabilize, stabilized, stabilizes, stabilizing stabilization INO:0000169 a regulation process that involves in two interactors that are synergized in affecting a phenomenon (e.g., phenotype). YH, ZX synergise, synergised, synergises, synergising, synergize, synergized, synergizes, synergizing synergization INO:0000171 a negative regulation that leads to a process termination. YH, ZX terminate, terminated, terminates, terminating termination INO:0000172 a gene expression regulation that leads to an increased rate of gene expression triggered either by biological processes or by artificial means. YH, ZX WEB: http://en.wikipedia.org/wiki/Transactivation trans-activate, trans-activated, trans-activates, trans-activating, trans-activation, trans-activator, trans-activators, transactivate, transactivated, transactivates, transactivating, transactivation, transactivator, transactivators transactivation INO:0000173 an interaction process that creates a complementary RNA copy of a sequence of DNA. YH WEB: http://en.wikipedia.org/wiki/Transcription_%28genetics%29 transcribe, transcribed, transcribes, transcribing, transcription gene transcription INO:0000174 a cell-cell interaction that transfers viral, bacterial, or both bacterial and viral DNA from one cell to another using a bacteriophage vector. YH, ZX transduce, transduced, transducer, transducers, transduces, transducing, transduction genetic transduction INO:0000176 A process that changes the location of a material entity. YH, ZX translocation, transloated, translocating, translocates, migrated, migration, migrates migrating, mobilization, mobilize, mobilized, mobilizes, mobilizing, mobilisation, mobilise, mobilised, mobilises, mobilising translocation INO:0000178 YH, ZX tyrosine-phosphorylated tyrosine-phosphorylation INO:0000231 a correlation association that two genes are co-expressed in a system. YH co-expression INO:0000234 a negative regulation that results in the deregulation of one interactor on a process. YH deregulation INO:0000235 A one-way interaction is an interaction that shows one direction between interactors. YH one-way interaction INO:0000241 a translocation that one interactor exports from one location YH export INO:0000242 a translocation that one interactor imports from one location YH import INO:0000244 a translocation that one interactor secretes from the inside of another interactor YH secretion INO:0000311 an interaction between two proteins. YH, ZX protein-protein interaction INO:0000312 an interaction that involves in a gene DNA and a protein YH, ZX gene-protein interaction LifO:0000005 An organism is an individual entity that exhibits the properties of life, including reproduction, growth and development, maintenance, and response to stimuli. All organisms are composed of one or more cells. https://en.wikipedia.org/wiki/Organism Oliver He An organism may be either a prokaryote or a eukaryote. Prokaryotes are represented by two separate domains—bacteria and archaea. Eukaryotic organisms are characterized by the presence of a membrane-bound cell nucleus and contain additional membrane-bound compartments called organelles. Viruses are not typically considered to be organisms because they are incapable of autonomous reproduction, growth or metabolism. organism Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues. acetylation PSI-MI MI:0192 acetylation reaction MI:0192 Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. It involves the addition of an amide group from a glycine to the target residue. amidation PSI-MI MI:0193 amidation reaction MI:0193 Covalent bond breakage in a molecule leading to the formation of smaller molecules. cleavage PSI-MI MI:0194 cleavage reaction MI:0194 Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners. PSI-MI MI:0195 covalent binding MI:0195 N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues. deacetylation PSI-MI MI:0197 deacetylation reaction MI:0197 S-farnesyl-L-cysteined is cleaved and returns a C residue. defarnesylation PSI-MI MI:0198 defarnesylation reaction MI:0198 N6-formyl-L-lysine is cleaved and returns a K residue. deformylation PSI-MI MI:0199 deformylation reaction MI:0199 S-geranylgeranyl-L-cysteine is cleaved and returns a C residue. degeranylation PSI-MI MI:0200 degeranylation reaction MI:0200 N6-myristoyl-L-lysine is cleaved and returns a K residue. demyristoylation PSI-MI MI:0201 demyristoylation reaction MI:0201 S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues. depalmitoylation PSI-MI MI:0202 depalmitoylation reaction MI:0202 Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues. dephosphorylation PSI-MI MI:0203 dephosphorylation reaction MI:0203 Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins. deubiquitination PSI-MI MI:0204 deubiquitination reaction MI:0204 Reversible reaction that can affect C residue. farnesylation PSI-MI MI:0206 farnesylation reaction MI:0206 Reaction that can affect K or G residues. Reside is functionalised with a formyl group. formylation PSI-MI MI:0207 formylation reaction MI:0207 An effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations. ab (not=) E PSI-MI MI:0208 genetic interaction MI:0208 Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue. geranylgeranylation PSI-MI MI:0209 geranylgeranylation reaction MI:0209 Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds. hydroxylation PSI-MI MI:0210 hydroxylation reaction MI:0210 Covalent or non covalent binding of lipid group on a protein residue. PSI-MI MI:0211 lipid addition MI:0211 Cleavage of a lipid group covalently bound to a protein residue. lipid cleavage PSI-MI MI:0212 lipoprotein cleavage reaction MI:0212 The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues. methylation PSI-MI MI:0213 methylation reaction MI:0213 Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues. myristoylation PSI-MI MI:0214 myristoylation reaction MI:0214 Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues. palmitoylation PSI-MI MI:0216 palmitoylation reaction MI:0216 Reversible reaction that can affect D,C,H,S,T,Y,R residues. phosphorylation PSI-MI MI:0217 phosphorylation reaction MI:0217 Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target. ubiquitination PSI-MI MI:0220 ubiquitination reaction MI:0220 Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred. PSI-MI MI:0403 colocalization MI:0403 Interaction between molecules that are in direct contact with each other. PSI-MI MI:0407 direct interaction MI:0407 Covalent bond mediated by 2 sulfur atoms. SS-bond disulfide bridge PSI-MI MI:0408 disulfide bond MI:0408 terms aiming to represent biochemical reactions referring to their resulting product modifications. Biochemical reaction PSI-MI MI:0414 enzymatic reaction MI:0414 Gln-Lys cross-link catalyzed by a transglutaminase. transglutamination PSI-MI MI:0556 transglutamination reaction MI:0556 Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues. adp ribosylation PSI-MI MI:0557 adp ribosylation reaction MI:0557 Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins. deglycosylation PSI-MI MI:0558 deglycosylation reaction MI:0558 The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate. glycosylation PSI-MI MI:0559 glycosylation reaction MI:0559 Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target. sumoylation PSI-MI MI:0566 sumoylation reaction MI:0566 Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target. neddylation PSI-MI MI:0567 neddylation reaction MI:0567 Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins. desumoylation PSI-MI MI:0568 desumoylation reaction MI:0568 Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome. deneddylation PSI-MI MI:0569 deneddylation reaction MI:0569 Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation. PSI-MI MI:0570 protein cleavage MI:0570 Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner. PSI-MI MI:0571 mrna cleavage MI:0571 Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments. PSI-MI MI:0572 dna cleavage MI:0572 The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand. DNA replication elongation dna elongation PSI-MI MI:0701 dna strand elongation MI:0701 An effect in which two genetic perturbations, when combined, result in a mutant phenotype that is not observed (to any degree) as a result of any of the individual perturbations. wt = a = b = E (not=) ab synthetic genetic interaction (sensu inequality) synthetic genetic interaction defined by inequality PSI-MI MI:0794 synthetic MI:0794 An effect in which individual perturbations of different genes and their combination result in the same mutant phenotype, to the same degree of severity/penetrance. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a = b = ab != wt where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. asynthetic asynthetic genetic interaction (sensu inequality) PSI-MI MI:0795 asynthetic MI:0795 An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than the most severe phenotype of the original perturbations, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab <= wt [E = a*] OR wt <= ab < a* [E = a*] where 'a*' is the most severe observed phenotype value of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. suppression suppressive genetic interaction (sensu inequality) PSI-MI Alleviating interaction MI:0796 suppression MI:0796 An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes. epistatic epistatic genetic interaction (sensu inequality) PSI-MI MI:0797 epistasis MI:0797 Reaction where a phosphate is transferred between two proteins of a phosphorelay system. phosphotransfer PSI-MI MI:0844 phosphotransfer reaction MI:0844 The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian. demethylation PSI-MI MI:0871 demethylation reaction MI:0871 Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate. triphosphatase react PSI-MI MI:0881 nucleoside triphosphatase reaction MI:0881 Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate. PSI-MI MI:0882 atpase reaction MI:0882 Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate. PSI-MI MI:0883 gtpase reaction MI:0883 Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner. PSI-MI MI:0902 rna cleavage MI:0902 Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments. ncl acid cleavage PSI-MI MI:0910 nucleic acid cleavage MI:0910 Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait. PSI-MI MI:0914 association MI:0914 Interaction between molecules within the same physical complex. Often identified under conditions which suggest that the molecules are in close proximity but not necessarily in direct contact with each other. PSI-MI MI:0915 physical association MI:0915 The observation that, when tested, no interaction was observed between two or more genes, for a given phenotype. In other words, the phenotype of the combined perturbations a and b result in the expected phenotype. noninteractive genetic interaction (sensu inequality) noninteractive genetic interaction defined by inequality PSI-MI MI:0932 noninteractive MI:0932 An effect in which two genetic perturbations, when combined, result in a phenotype that is more severe/penetrant than expected given the phenotypes of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < E <= wt OR wt <= E < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. negative gen int PSI-MI MI:0933 negative genetic interaction MI:0933 An effect in which the observed phenotype of individual perturbations and/or the double perturbation collectively exhibit values both greater than AND less than wild type (on the same scale). Alternatively, this could describe a scenario in which individual perturbations result in qualitatively different phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < wt < b [ab != E] OR With respect to two qualitatively different phenotypes, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively different phenotypes. neutral gent int PSI-MI MI:0934 neutral genetic interaction MI:0934 An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than would be expected from the original phenotypes, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: E < ab <= wt OR wt <= ab < E where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. positive gent int PSI-MI MI:0935 positive genetic interaction MI:0935 An oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. redox reaction PSI-MI MI:0945 oxidoreductase activity electron transfer reaction MI:0945 The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine. orchard 2009-10-28T01:20:40Z p_patetheinylation PSI-MI MI:0971 phosphopantetheinylation MI:0971 The removal of an amine group from a molecule. orchard 2010-04-26T10:49:06Z deamination PSI-MI MI:0985 deamination reaction MI:0985 The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase. orchard 2010-04-26T10:52:22Z strand elongation PSI-MI MI:0986 nucleic acid strand elongation reaction MI:0986 The process by which an RNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent RNA strand. orchard 2010-04-26T11:00:08Z rna elongation PSI-MI MI:0987 rna strand elongation MI:0987 A modification that converts an L-histidine residue to diphthamide. orchard 2010-11-11T12:36:51Z diphthamidation PSI-MI MI:1027 diphtamidation reaction MI:1027 Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method. orchard 2011-08-03T11:14:11Z predicted PSI-MI MI:1110 predicted interaction MI:1110 Intra-molecular interaction between two or more regions of the same molecule. orchard 2012-01-03T01:19:22Z PSI-MI MI:1126 The corresponding experimental role will be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information. self interaction MI:1126 Interaction between two or more regions of possibly the same molecule but it is also possible that the observation is due to an interaction between two identical molecules. orchard 2012-01-03T01:21:58Z PSI-MI MI:1127 The corresponding experimental role should be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information. putative self interaction MI:1127 Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins. orchard 2012-01-03T03:24:05Z carboxylation PSI-MI MI:1139 carboxylation reaction MI:1139 Decarboxylation is a chemical reaction that releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1). orchard 2012-01-03T03:31:42Z decarboxylation PSI-MI MI:1140 decarboxylation reaction MI:1140 Aminoacylation is the process of adding an aminoacyl group to a compound. orchard 2012-01-03T03:49:50Z aminoacylation PSI-MI MI:1143 aminoacylation reaction MI:1143 Measurement of the hydrolysis of phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze. orchard 2012-01-03T04:08:14Z PSI-MI MI:1146 phospholipase reaction MI:1146 AMPylation, previously known as adenylylation, is formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids. orchard 2012-01-03T04:21:12Z ampylation PSI-MI MI:1148 ampylation reaction MI:1148 The formation of a phosphodiester or phosphoramide ester of UMP and amino acid (MOD:01166). orchard 2012-08-10T07:50:08Z uridylation PSI-MI umpylation MI:1230 uridylation reaction MI:1230 The conversion between cis- and trans- peptide bonds formed by the amine group of a proline. orchard 2012-08-10T09:02:28Z PSI-MI MI:1237 proline isomerization reaction MI:1237 The catalysis of the structural rearrangement of isomers. orchard 2012-08-10T12:51:00Z PSI-MI MI:1250 isomerase reaction MI:1250 The catalysis of the conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2. orchard 2012-08-10T01:23:35Z PSI-MI MI:1251 methylmalonyl-CoA isomerase reaction MI:1251 An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation to a severity/penetrance beyond (further from wild type) that expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < E < wt OR wt < E < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T19:12:17Z PSI-MI Aggravating interaction MI:1271 enhancement MI:1271 An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in the same direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ((a* < b < wt) OR (wt < b < a*)) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:05:15Z PSI-MI MI:1272 positive epistasis MI:1272 An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab = a* < b < wt OR wt < b < a* = ab where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:11:27Z PSI-MI MI:1273 maximal epistasis MI:1273 An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the least severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab = b < wt OR wt < b = ab < a* where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:13:14Z PSI-MI MI:1274 minimal epistasis MI:1274 An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are EITHER traits measured on the same quantitative scale but each significantly deviating, in opposite directions, from wild type, OR completely (qualitatively) different phenotypes), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) OR (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value, and 'a != b' indicates qualitatively different phenotypes. orchard 2013-06-05T20:22:53Z PSI-MI MI:1275 neutral epistasis MI:1275 An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:25:26Z psi-mi:MI:1285 PSI-MI MI:1276 opposing epistasis MI:1276 An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits that cannot be measured on the same scale and, hence, qualitatively different), and the resulting phenotype of their combination is equal to that of only one of the perturbations. This may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotypes of the individual perturbations, 'ab' is the observed phenotype of the double perturbation, 'wt' is the wild type phenotype and 'a != b' indicates qualitatively different phenotypes. orchard 2013-06-05T20:26:38Z PSI-MI MI:1277 qualitative epistasis MI:1277 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is more severe/penetrant (further from wild type) than expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < a* <= b < wt [E = a*] OR wt < b <= a* < ab [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:31:30Z PSI-MI MI:1278 mutual enhancement MI:1278 An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation (which, on its own, has no effect on the phenotype in question) to a severity/penetrance beyond (further from wild type) that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < a < b = wt [E = a] OR wt = b < a < ab [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:33:13Z PSI-MI MI:1279 unilateral enhancement MI:1279 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (a* < ab <= wt) [E = a*] OR (wt < b <= a*) AND (wt <= ab < a*) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:35:53Z PSI-MI MI:1280 mutual suppression MI:1280 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting combination is wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* <= b < ab = wt OR wt = ab < b <= a* OR a < wt = ab < b where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:37:41Z PSI-MI MI:1281 mutual suppression (complete) MI:1281 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected, but not wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (a* < ab < wt) [E = a*] OR (wt < b <= a*) AND (wt < ab < a*) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:39:12Z PSI-MI MI:1282 mutual suppression (partial) MI:1282 An effect in which individual perturbations of different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination has a phenotype more severe/penetrant than the least severe/penetrant and less severe/penetrant than the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab < b < wt [E = a*] OR wt < b < ab < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:43:52Z PSI-MI MI:1283 suppression-enhancement MI:1283 An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in any direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates quantitatively different phenotypes. orchard 2013-06-05T20:47:35Z PSI-MI MI:1284 quantitative epistasis MI:1284 An effect in which the observed phenotype of a double perturbation is opposite (relative to the wild type phenotype) to that which is expected upon the double perturbation. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < wt < E OR E < wt < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:04:18Z PSI-MI MI:1286 over-suppression MI:1286 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is opposite (relative to wild type) to that expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* <= b < wt < ab [E = a*] OR ab < wt < b <= a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:06:09Z PSI-MI MI:1287 mutual over-suppression MI:1287 An effect in which two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is more severe than the phenotype observed with the same directionality. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < wt < b < ab OR ab < a < wt < b where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:11:03Z PSI-MI MI:1288 over-suppression-enhancement MI:1288 An effect when two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is intermediate to the individual mutant phenotypes, but greater or less than wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (a < ab < b) AND (ab != wt) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:15:34Z PSI-MI MI:1289 phenotype bias MI:1289 An effect in which the perturbation of one gene results in complete suppression (to wild type) of the mutant phenotype caused by perturbation of another gene. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: wt = ab != a = E where 'a' is the observed phenotype values of an individual perturbation, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:34:57Z PSI-MI MI:1290 suppression (complete) MI:1290 An effect in which the perturbation of one gene results in the amelioration or lessening of the severity/penetrance of a mutant phenotype caused by perturbation of another gene, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab < wt [E = a*] OR wt < ab < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:36:07Z PSI-MI MI:1291 suppression (partial) MI:1291 An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab <= b = wt [E = a] OR wt = b <= ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:37:28Z PSI-MI MI:1292 unilateral suppression MI:1292 An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the complete suppression (to wild type) of the mutant phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab = b = wt [E = a] OR wt = b = ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:38:36Z PSI-MI MI:1293 unilateral suppression (complete) MI:1293 An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab < b = wt [E = a] OR wt = b < ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:39:32Z PSI-MI MI:1294 unilateral suppression (partial) MI:1294 An effect in which the perturbation of one gene (which has no individual effect on the phenotype in question), when combined with a perturbation of another gene (which causes the phenotype in question), results in a mutant phenotype opposite (relative to wild type) to that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: E = a < b = wt < ab OR ab < wt = b < a = E where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:54:08Z PSI-MI MI:1295 unilateral over-suppression MI:1295 Measure of hydrolytic reactions that release ADP-ribose. orchard 2013-06-06T10:34:18Z PSI-MI mono-ADP-ribosylhydrolase reaction MI:1310 de-ADP-ribosylation reaction MI:1310 Reaction where a sulfate group is transferred between two proteins orchard 2014-01-08T11:16:12Z sulfurtransfer sulphurtransfer reaction PSI-MI MI:1327 sulfurtransfer reaction MI:1327 Reaction monitoring the cleavage (hydrolysis) or a lipid molecule. orchard 2015-02-03T13:25:21Z PSI-MI MI:1355 lipid cleavage MI:1355 The process mediated by guanine nucleotide exchange factors (GEFs) that catalyze the exchange of bound GDP with cytosolic GTP. ppm 2017-01-19T16:13:36Z GEF reaction PSI-MI MI:2252 guanine nucleotide exchange factor reaction MI:2252 Reaction that create a covalent bond between a nitrogen monoxide group and the thiol group of cysteine. ppm 2017-01-19T17:11:46Z s-nitrosylation PSI-MI MI:2263 s-nitrosylation MI:2263 Reversible reaction that add a tyrosine residue to an amino-acid. ppm 2017-01-26T15:21:43Z GO:GO:0018322 tyrosinylation PSI-MI MI:2272 tyrosinylation MI:2272 Reversible reaction that add a tyrosine residues to the c-terminal end of alpha-tubulin. ppm 2017-01-26T15:22:39Z GO:GO:0018166 tyrosination PSI-MI MI:2273 tyrosination MI:2273 Reaction in which an amide functional group in the side chain of the amino acids asparagine or glutamine is removed or converted to another functional group. Typically, asparagine is converted to aspartic acid or isoaspartic acid and glutamine is converted to glutamic acid or pyroglutamic acid (5-oxoproline). ppm 2017-08-08T14:38:29Z deamidation PSI-MI MI:2280 deamidation reaction MI:2280 NCBITaxon:1773 NCBITaxon:2528440 GC_ID:11 PMID:29205127 ncbi_taxonomy Bacillus tuberculosis Bacterium tuberculosis Mycobacterium tuberculosis typus humanus Mycobacterium tuberculosis var. hominis Mycobacterium tuberculosis variant tuberculosis Mycobacterium tuberculosis NCBITaxon:2 GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11542017 PMID:11542087 PMID:11760965 PMID:12054223 PMID:2112744 PMID:270744 PMID:7520741 PMID:8123559 PMID:8186100 PMID:8590690 PMID:9103655 PMID:9336922 eubacteria ncbi_taxonomy Monera Procaryotae Prokaryota Prokaryotae bacteria prokaryote prokaryotes Bacteria NCBITaxon:2157 GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11541975 PMID:11542064 PMID:11542149 PMID:11760965 PMID:12054223 PMID:2112744 PMID:25527841 PMID:270744 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 ncbi_taxonomy Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes Archaea NCBITaxon:2759 GC_ID:1 PMID:23020233 PMID:30257078 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes Eukaryota NCBITaxon:562 NCBITaxon:1637691 NCBITaxon:1806490 NCBITaxon:469598 NCBITaxon:662101 NCBITaxon:662104 GC_ID:11 PMID:10319482 E. coli Escherichia/Shigella coli ncbi_taxonomy Bacillus coli Bacterium coli Bacterium coli commune Enterococcus coli Escherichia coli NCBITaxon:9606 GC_ID:1 human ncbi_taxonomy Homo sapiens OGG:0000000002 A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule. Oliver He WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/ gene An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. natural protein native protein protein PR:000000001 The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. protein PR:000000001 A pathway is a set of inter-connected reactions and interactions whose delineation and scope are used as a model for exploring and studying, describing and understanding the working of and relationships between biomolecules within a context. pathway PW:0000001 pathway PW:0000001 The various, enzyme controlled, series of reactions allowing for the conversion of materials, energy availability and biodegradation of xenobiotics. pathway PW:0000002 The definition was compiled based on a number of available defintions in various dictionaries. classic metabolic pathway PW:0000002 The pathways where a signal - hormone, neurotransmitter, growth factor, peptide, any molecule - triggers one or multiple cascades of events. This involves a number of molecules, including receptors, proteins, ligands, messengers, any participating molecule. A signaling pathway may be upstream or downstream of other signaling pathways. Signaling pathways control a very broad spectrum of processes as well as pathways. pathway PW:0000003 The definition was compiled based on a number of definitions available in various dictionaries. signaling pathway PW:0000003 The pathways that control the processes by which a cell or organism develops, adjusts, behaves, responds to conditions or changes in these conditions, or in any manner helps promote and maintain its efficient functioning. pathway PW:0000004 The definition was complied based on a number of definitions available in several dictionaries regulatory pathway PW:0000004 Complex human diseases encompass a spectrum of genetic and environmental attributes that together affect the normal functioning of several molecular and cellular pathways. Their combined and accumulated effect is manifested in the anomalous phenotype of the complex condition. pathway complex human diseases PW:0000013 disease pathway PW:0000013 The pharmacokinetics and the pharmacodynamics pathway elicited by the administration of specific drugs. The systems involved in drug processing and responses are also those handling exogenous, xenobiotic compounds in the cellular detoxification pathway. The distinction between a random encounter with a foreign compound and the processing of a substance administered for treatment along with the importance of genetic variation for the individual responses to particular drugs warrant their separate consideration. VPetri 2010-03-15T11:01:15Z pathway PW:0000754 drug pathway PW:0000754 1.1.13 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) 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 has part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in A host-pathogen interaction that has a specific interaction type (e.g., activation). An object property that represents a relation between an interaction process (domain) and another interaction process (range) where the interaction proces (domain) has a specific type of the other interaction process (range) Yongqun He has interaction type 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 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 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 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 Product version Yu Lin (YL) Arzucan Ozgur Junguk Hur Yongqun "Oliver" He (YH) Zuoshuang "Allen" Xiang 2022-03-27 he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles. OWL-DL An ontology of interactions and interaction networks INO: Interaction Network Ontology 1.1.13