]> 2018-01-10 INO: Interaction Network Ontology Junguk Hur Yu Lin (YL) Arzucan Ozgur An ontology for the annotation of the interaction network domain. OWL-DL Product version The Interaction Network Ontology (INO) is an ontology in the domain of interaction network. INO aims to standardize interaction network annotation, integrate various interaction network data, and support computer-assisted reasoning. It is aimed to represent general interactions (e.g., molecular interactions) and interaction networks (e.g., Bayesian network). INO was initiated by supporting literature mining related to interactions and interaction networks. INO aligns with BFO. INO is a community-based ontology. Its development follows the OBO Foundry principles. Vision Release; 1.0.107 Yongqun "Oliver" He (YH) Zuoshuang "Allen" Xiang BFO OWL specification label Really of interest to developers only 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. BFO CLIF specification label Person:Alan Ruttenberg Really of interest to developers only Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 editor preferred term GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) editor preferred term 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. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober example has curation status OBI_0000281 PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition textual definition textual definition definition definition 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. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober 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. 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. GROUP:OBI:<http://purl.obfoundry.org/obo/obi> PERSON:Daniel Schober editor note term editor 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. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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 PERSON:Daniel Schober term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober alternative term definition source Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober 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 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: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 person:Alan Ruttenberg has associated axiom(nl) has associated axiom(fol) An axiom expressed in first order logic using CLIF syntax Person:Alan Ruttenberg Person:Alan Ruttenberg has associated axiom(fol) has literature mining keywords Yongqun He 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. example of literature mining keyword usage an example of usage for literature mining Yongqun He literature mining example has keyword dependency pattern Arzucan Ozgur, Junguk Hur, Yongqun He an annotation property that specifies the dependency pattern of the literature keywords that match to the ontology interaction type. temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime 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. logical macro assertion https://github.com/oborel/obo-relations/wiki/ShortcutRelations 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 on a property A logical macro assertion whose domain is an IRI for a property logical macro assertion on an object property logical macro assertion on an annotation property is direct form of Chris Mungall 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' is indirect 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 Contributor An entity responsible for making contributions to the content of the resource. 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. Coverage 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. Creator An entity primarily responsible for making the content of the resource. 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. Date A date associated with an event in the life cycle of the resource. 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. Description An account of the content of the resource. 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. Format The physical or digital manifestation of the resource. 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). Resource Identifier An unambiguous reference to the resource within a given context. 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). Language A language of the intellectual content of the resource. 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. Publisher An entity responsible for making the resource available 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. Relation 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. Rights Management 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. Source A reference to a resource from which the present resource is derived. 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. Subject and Keywords The topic of the content of the resource. 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. Title Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Resource Type The nature or genre of the content of the resource. 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. database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym in_subset is defined by label part of 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. http://www.obofoundry.org/ro/#OBO_REL:part_of Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. a core relation that holds between a part and its whole 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) part_of this day is part of this year (occurrent parthood) has part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. a core relation that holds between a whole and its part has part 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) realized in 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 [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]) is realized by realized in 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 realizes Paraphrase of elucidation: a relation between a process and a realizable entity, 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 realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility 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]) obsolete preceded by accidentally included in BFO 1.2 proposal - should have been BFO_0000062 preceded by 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. http://www.obofoundry.org/ro/#OBO_REL:preceded_by is preceded by preceded by 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. precedes 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. has activator Yongqun He an object property between an activation process and a material entity that acts as an activator during the process. has_controller controls has_next_step lacks part has interaction type 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) A host-pathogen interaction that has a specific interaction type (e.g., activation). Yongqun He inheres in A dependent inheres in its bearer at all times for which the dependent exists. a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence inheres in inheres_in this fragility inheres in this vase this red color inheres in this apple bearer of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence bearer of bearer_of is bearer of this apple is bearer of this red color this vase is bearer of this fragility participates in a relation between a continuant and a process, in which the continuant is somehow involved in the process participates in participates_in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation has participant Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. a relation between a process and a continuant, in which the continuant is somehow involved in the process has participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has_participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) has role 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. a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence has_role this person has role this investigator role (more colloquially: this person has this role of investigator) has component activity 2017-05-24T09:44:33Z dos A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component process 2017-05-24T09:49:21Z dos w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. has effector activity 2017-09-22T14:14:36Z dos This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. before or simultaneous with <= David Osumi-Sutherland Primitive instance level timing relation between events simultaneous with David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) before David Osumi-Sutherland t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) during which ends 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. encompasses 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. di David Osumi-Sutherland ends after David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) immediately preceded by starts_at_end_of David Osumi-Sutherland X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) during which starts 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. starts before David Osumi-Sutherland immediately precedes ends_at_start_of meets David Osumi-Sutherland X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) starts during David Osumi-Sutherland X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) io happens during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) d during David Osumi-Sutherland ends 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). overlaps http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) x overlaps y if and only if there exists some z such that x has part z and z part of y has component For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. regulates false David Hill Tanya Berardini Regulation precludes parthood; the regulatory process may not be within the regulated process. Chris Mungall regulates (processual) GO 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 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. negatively regulates Chris Mungall 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. negatively regulates (process to process) positively regulates positively regulates (process to process) 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 temporally related to https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 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. A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. starts Chris Mungall inverse of starts with Allen starts with Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor started by Chris Mungall 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. ends inverse of ends with Chris Mungall ends with Chris Mungall finished by 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. has input 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 output Chris Mungall p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. produces 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 increases the frequency, rate or extent of y causally upstream of, negative 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 inheres in part of q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. Chris Mungall Because part_of is transitive, inheres in is a sub-relation of inheres in part of mereotopologically related to A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships functionally related to Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function regulated by inverse of regulates Chris Mungall regulated by (processual) negatively regulated by Chris Mungall inverse of negatively regulates positively regulated by inverse of positively regulates Chris Mungall input of Chris Mungall inverse of has input output of inverse of has output Chris Mungall has direct input 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' Chris Mungall obsolete has direct output true p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. translation SubClassOf has_direct_output some protein Chris Mungall directly produces causally downstream of inverse of upstream of Chris Mungall immediately causally downstream of Chris Mungall directly activates directly positively regulates 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 directly activates (process to process) Chris Mungall indirectly activates indirectly positively regulates Chris Mungall 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 directly inhibits directly negatively regulates directly inhibits (process to process) Chris Mungall indirectly inhibits indirectly negatively regulates Chris Mungall causally related to This relation groups causal relations between material entities and causal relations between processes 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. 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. causally upstream of Chris Mungall p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain immediately causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall directly provides input for Chris Mungall directly provides input for (process to process) 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 transitively provides input for Chris Mungall transitive form of directly_provides_input_for 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) causally upstream of or within influences (processual) Chris Mungall 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 affects causally downstream of or within Chris Mungall inverse of causally upstream of or within causal relation between processes Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall 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. depends on Chris Mungall directly regulates Chris Mungall directly regulates (processual) 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. related via dependence to A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. directly positively 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 negatively regulates directly negatively regulates (process to process) 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. entity entity 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 An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) 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 Julius Caesar Verdi’s Requiem the Second World War your body mass index continuant continuant Continuant (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. 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 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]) occurrent (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region 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. (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] 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]) 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 occurrent Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) 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. b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) independent continuant IndependentContinuant (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] (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) ic a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism 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]) the bottom right portion of a human torso the interior of your mouth temporal region (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] TemporalRegion t-region (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] 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]) 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 process Process (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] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. 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) a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping 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]) process the course of a disease the flight of a bird the life of an organism your process of aging. disposition (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] 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. Disposition (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] disposition 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]) an atom of element X has the disposition to decay to an atom of element Y 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]) 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 realizable entity (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] (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] A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) RealizableEntity 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]) realizable 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 quality (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] quality Quality (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] 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]) 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]) 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 specifically dependent continuant (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] A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. 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 SpecificallyDependentContinuant 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. 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]) 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. sdc 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 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. Role role (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] 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. 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. 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]) 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 site site Site (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] 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 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]) 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) object object Object 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 atom 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]) cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star generically dependent continuant (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] GenericallyDependentContinuant gdc 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. 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]) 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. function (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] Function 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]) 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. 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 one-dimensional temporal region (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] OneDimensionalTemporalRegion 1d-t-region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) 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). the temporal region during which a process occurs. material entity material (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 y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] (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] 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]) 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 MaterialEntity 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: 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. Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) 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 every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) the undetached arm of a human being immaterial entity immaterial 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 ImmaterialEntity zero-dimensional temporal region (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] ZeroDimensionalTemporalRegion 0d-t-region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) a temporal region that is occupied by a process boundary right now temporal instant. the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. cell cell 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 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). VHOG:0001533 WBbt:0004017 XAO:0003012 cell epithelial cell 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 cell epitheliocyte macrophage 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 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. cell histiocyte protein complex assembly GO:0006461 The aggregation, arrangement and bonding together of a set of components to form a protein complex. biological_process protein complex formation protein acetylation GO:0006473 The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. biological_process protein amino acid acetylation apoptotic process 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. GO:0006915 activation of apoptosis apoptosis apoptosis signaling apoptotic cell death apoptotic program apoptotic programmed cell death biological_process programmed cell death by apoptosis type I programmed cell death biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. GO:0008150 biological process biological_process physiological process cell death 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). GO:0008219 biological_process programmed cell death 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. GO:0012501 biological_process caspase-independent cell death non-apoptotic programmed cell death nonapoptotic programmed cell death phosphorylation GO:0016310 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 protein myristoylation GO:0018377 The covalent attachment of a myristoyl group to a protein. biological_process protein amino acid myristoylation protein oligomerization GO:0051259 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. biological_process protein oligomer assembly protein oligomer biosynthesis protein oligomer biosynthetic process protein oligomer formation data item 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/ 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. Data items include counts of things, analyte concentrations, and statistical summaries. 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 a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. data data item information content entity 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). A generically dependent continuant that is about some thing. Examples of information content entites include journal articles, data, graphical layouts, and graphs. OBI_0000142 PERSON: Chris Stoeckert information content entity 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. pathogen role 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. Alexander Diehl 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. Albert Goldfain Lindsay Cowell pathogen A material entity with a pathogenic disposition. Alexander Diehl Lindsay Cowell Albert Goldfain host role A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism. Alexander Diehl Lindsay Cowell Albert Goldfain interaction network 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 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 is a processual entity that has two or more participants (i.e., interactors) that have an effect upon one another. pathway an interaction network that includes at least two interactions and has a start point(s) and an end point(s). YH, ZX Bayesian network YH, ZX 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). WEB: http://en.wikipedia.org/wiki/Bayesian_network regulator role an regulator role that is borne by a material entity that regulates an interaction. YH up-regulation YH a positive regulation that one interactor up-regulates another. up-regulate, up-regulations, up-regulated, up-regulating, upregulate, upregulations, upregulated, upregulating interaction regulator an interactor that regulates an interaction. YH input interactor role YH, ZX interaction input role an interactor role that is borne by a material entity that acts as an input of an interaction. output interactor role interaction output role an interactor role that is borne by a material entity that acts as an output of an interaction. YH, ZX activator role YH a positive regulator role that is borne by a material entity that activates an interaction. mutual information network WEB: http://en.wikipedia.org/wiki/Mutual_information an interaction network model that is represented by at least two mutual information interactions. YH, ZX node YH, ZX is node equal to interactor?? (YL) a node is an object that represents an interactor in a graph of an interaction or interaction network. edge YH, ZX an edge is an object that represents a graphic line that links two interactors in an interaction. interactor role YH, ZX a role that is borne by a material entity to act as a participant in an interaction process. interactor an interactor is a material entity that participates in an interaction. YL. YH. ZX. activator a positive interaction regulator that activates an interaction. YH organism-organism interaction YL.YH. ZX. a biological interaction that occurs in the organism level. Examples: a bacterium interacts with a mouse, a cat interacts with a dog two-way interaction A two-way interaction is an interaction that includes two different directions among two interactors. YH human molecular pathway YH, ZX a pathway that exists in human body. up-regulation of secretion YH an up-regulation that one interactor up-regulates the secretion of another interactor. up-regulate, up-regulations, up-regulated, up-regulating, upregulate, upregulations, upregulated, upregulating human molecular interaction YH, ZX an interaction involving human molecules YH: This branch may be made obsolete since we now have human INO (HINO). activation YH, ZX a positive regulation that one interactor activates another. activate, activated, activates, activating, activation, activator, activators, activity gene-cell interaction an interaction that includes a gene and a cell as interactors. YL.YH. ZX. protein activation protein activation, protein activated, activates protein, activating protein, activated protein an activation process where one protein is activated by a material entity YH YH: in literature mining, the protein can be any specific protein symbol or protein name. cell-cell interaction a biological interaction that involves two cells as interactors. YL.YH. ZX. protein activation by mutant protein activation by gene mutant YH an activation process where one protein is activated by a gene mutant 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, protein activated by mutant, mutant activates protein, activating protein by mutant, mutant activated protein antagonism antagonise, antagonised, antagonises, antagonising, antagonist, antagonists, antagonize, antagonized, antagonizes, antagonizing YH, ZX a biochemical binding where a substance binds to the same site an agonist would bind to without causing activation of the receptor WEB: http://en.wikipedia.org/wiki/Receptor_antagonist gene-enviroment interaction YL.YH. ZX. an interaction that involves a gene and its environment (e.g., calcium in blood). regulation of protein location "Localization of SpoIIE was shown to be dependent on the essential cell division protein FtsZ" (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10747015) location // (protein) // dependent, location // (protein) // depends YH, AO a regulation process that regulates the location of a protein regulation of transcription a gene expression regulation process that involves the regulation of a 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 regulation of gene transcription YH, AO, JH 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) attenuation attenuate, attenuated, attenuates, attenuating YH, ZX a negative regulation that attenuates the virulence of a pathogenic microbe. regulation of translation regulation of gene translation translation depends, translation // dependent, regulates // translation, regulated // translation, regulates the translation of, regulated the translation of, regulation // production, regulated // production, regulate // production YH, AO a gene expression regulation process that involves the regulation of a protein translation process. "Transcription of ydhD was dependent on SigE" (Reference: http://www.ncbi.nlm.nih.gov/pubmed/11011148) regulation of protein translation autophosphorylation YH, ZX a phosphorylation process that adds a phosphate to a protein kinase (possibly affecting its activity) by virtue of its own enzymic activity. autophosphorylate, autophosphorylated, autophosphorylates, autophosphorylating, autophosphorylation regulation of gene 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) YH, AR, JH WEB: http://www.medilexicon.com/medicaldictionary.php?t=970 a regulation process that regulates the activation of a gene so that the gene is expressed at a particular time essential for // activation, essential for // activation, activated // expression, activates // expression, control // activation, controlling // activation, requires // activation, requiredd // activation positive regulation of gene expression a regulation process that positively regulates gene expression level positive regulation // expression, increase // expression, induced // dependent, induced // via, induced // by, induced // dependent // presence YH, AR "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) negative regulation of gene expression "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) YH, AR essential for // negative regulation, negatively regulated // expression, negatively regulates // expression, negative regulator // transcription a regulation process that negatively regulates gene expression level human biochemical reaction a human molecular reaction that is specifically a biochemical reaction YH. ZX physical entity place holder for physical entities negative regulation of gene transcription 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 protein translation a negative regulation process that down-regulates protein translation level negatively regulated // translation, negatively regulates // translation, limits // production, limited // production YH, AO gene expression regulation regulation of gene expression YH, AO, JH a regulation process that regulates gene expression level amod(expression, dependent) "SigK and GerE were essential for ykvP expression" (Reference: http://www.ncbi.nlm.nih.gov/pubmed/11011148) 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 protein translation translation, translated, translating, encoding, encodes, protein production gene translation a gene expression process that results in protein production from a gene DNA sequence. YH, ZX WEB: http://en.wikipedia.org/wiki/Translation_%28biology%29 inhibition of gene transcription YH, AO inhibited // transcription, inhibits // transcription, repressed // transcription, repress // transcription, prevented // transcription, prevents // transcription, prevent // transcription a negative regulation of gene transcription process that specifiies the negative regulation being an inhibition. "GerE protein inhibits transcription in vitro of the sigK gene." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739) chemical reaction catalyst an interactor that starts or speeds up a chemical reaction while undergoing no permanent change itself. YH coimmunoprecipitation co-immunoprecipitation YH, ZX a coprecipitation that occurs through an immunoprecipitation process. 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 positive regulation of gene transcription positively regulated // transcription, negatively regulates // transcription, stimulating // transcription, stimulates // transcription, stimulated // transcription, induction // transcription, induced // transcription, induces // transcription, inducing // transcription, driven // transcription, drives // transcription a regulation of transcription process that inviolves a positive regulation. YH, AO dobj(stimulating,transcription) competition an indirect association that one interactor competes with another interactor in a specfiic process. YH, ZX compete, competed, competes, competing activation of gene transcription a positive regulation of gene transcription process that inviolves an activation of the gene transcription. activated // transcription, activates // transcription YH, AO "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 by low level protein "A low level of GerE activated transcription of cotD by sigmaK." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739) an activation of gene transcription that is achieved by a low level of a protein low level // activated // transcription, low level // activates // transcription, low concentration // activated // transcription YH, AO positive regulation of protein translation YH, AO a regulation of translation process that positively regulates protein translation level "ComK ... thereby increasing the production of the FlgM." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/9696775) positively regulated // translation, positively regulates // translation, increases // production, increased // production, increasing // production, increasing // production antigen-antibody interaction WEB: http://en.wikipedia.org/wiki/Antigen-antibody_interaction YH a direct interaction where an antigen interacts with an antibody physically. regulation of protein activity YH, AO 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) protein activity regulation regulated // activity, regulates // activity, essential // activity, controlled // activity, controls // activity, activity under control, essential for // activity a regulation process that regulates an activity of a protein downexpression a gene expression that has decreased volume. decreased gene expression YH, ZX controling YH, ZX a regulation that one interactor controls the quality of another interactor to a specific range control, controled, controling, controlled, controlling, controls conversion conversion, convert, converted, converting, converts, derived, derives, derivation a direct physical association that one interactor is converted from another interactor. YH, ZX cooperation an indirect association that one interactor cooperates with another interactor in a specfiic process. cooperate, cooperated, cooperates, cooperating YH, ZX coprecipitation 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 YH, ZX a colocalization that two interactors are precipitated together. correlation YH, ZX an indirect association that two interactors are correlated in a process without defined influence of each other. correlate, correlated, correlating costimulation costimulate, costimulated, costimulating YH, ZX, AO 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. cell-environment interaction an interaction that involves a cell and its environment as interactors YH cross-immunoprecipitation interaction YH, ZX an immuno-precipitation that one interactor is precipitated based on an cross- immunological precipitation process. cross-immunoprecipitate, cross-immunoprecipitated, cross-immunoprecipitates, cross-immunoprecipitating, cross-immunoprecipitation, crossimmunoprecipitate, crossimmunoprecipitated, crossimmunoprecipitates, crossimmunoprecipitating, crossimmunoprecipitation organism-environment interaction an interaction that involves an organism and its environment as interactors YH immunological cross-reaction YH, ZX an antigen-antibody interaction where an antibody interats with an antigen that differs from the immunogen used to generate antibody. negative regulation of protein activity negative protein activity regulation a regulation of protein activitiy process that involves a negative regulation negatively regulated // activity, negatively regulates // activity YH, AO negative regulation YH, ZX a regulation in which one interactor has a negative effect on another interactor down-regulate, down-regulations, down-regulated, down-regulating, downregulate, downregulations, downregulated, downregulating YH: different types of negative regulations exist. These types are related to different qualities and phenotyes of regulated targets. chemical reaction catalyst role YH an interactor role that is played by a material entity that starts or speeds up a chemical reaction while undergoing no permanent change itself. inhibition of protein activity inhibited // activity, inhibites // activity, inhibition // activity YH, AO "... FlgM antisigma factor that inhibits sigmaD activity." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/9696775) a negative regulation of protein activitiy process that involves an inhibition of a protein activity regulation of transcription by binding to promoter 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 a regulation of transcription process that occurs through the binding to a promotor of a gene 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). YH, AO "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) positive regulation of transcription by binding to promoter a regulation of transcription by binding to promoter that is further classified as a positive regulation YH, AO "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) 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 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). decrease reduction decrease, decreased, decreases, decreasing, decreasing, reduce, reduced, reduces, reducing, diminish, diminished, diminishes, diminishing, declining, declines, declination, limit, limited, limiting, limits a negative regulation that results in the decrease of one interactor volume. YH, ZX negative regulation of transcription by binding to promoter negatively regulate // promoter, negatively regulated // promoter, repressed // promoter, represses // promoter, repress // promoter, binds // transcriptional start site // repressor, bound // transcriptional start site // repressor 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). "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) a regulation of transcription by binding to promoter that is further classified as a positive regulation YH, AO gene activation activation // (gene), activated // (gene), activates // // (gene), activated // action 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 biochemical degradation an enzymatic reaction that leads to the breakdown of a biochemical entity. degradation, degradations, degrade, degraded, degrades, degrading YH, ZX co-regulation of transcription YH, AO transcription // combined action, transcription // results from // combined action a regulation of transcription process where two or more regulators regulate a gene transcription "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) activation of gene transcription by high level protein "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) 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 promoter-based regulation of transcription 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). 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) a regulation of transcription process through binding to a promoter or regulating the promoter binding activity activation of gene transcription by phosphorylated protein phosphorylated // activator // transcription, phosphorylated // activates // transcription, phosphorylated // activate // transcription, phosphorylated // activated // transcription YH, AO "Spo0A, which when phosphorylated is an activator of sigE transcription." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10383978) an activation of gene transcription that is achieved by a phosphorylated protein human molecular catalysis YH destabilization a negative regulation that results in a destabilization. YH, ZX destabilization, destabilize, destabilized, destabilizes, destabilizing gene expression inhibition a negative regulation process that inhibits gene expression level 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) YH dominant regulation YH, ZX determine, determined, determines, determining, cause, caused, causes, causing, lead, leading, leads, led, govern, governed, governing, governs a regulation that one interactor has a dominant effect on the quality of another interactor. This differs from the accessory regulation. protein dimerization YH, ZX a protein complex assembly that involves two proteins that form a dimer. dimerize, dimerized, dimerizes, dimerizing co-regulation co-regulation, co-regulated, co-regulate, co-regulating YH a regulation process that involves in two interactors co-regulate a third interactor. molecular complex disruption a negative regulation that results in a disruption. YH, ZX disrupt, disrupted, disrupting, disrupts dissociation dissociate, dissociated, dissociating, dissociation YH, ZX down-regulation 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 a negative regulation that one interactor down-regulates another. YH, ZX gene expression up-regulation essential for // up-regulation, up-regulated // expression, up-regulates // expression a positive regulation of gene expression process that up-regulates gene expression level YH, AR gene expression down-regulation a negative regulation process that down-regulates gene expression level YH down-regulated // expression, down-regulates // expression induction of production an induction that leads to the production of an entity induction of the production, induces the production, induced the production YH YH: For example, "IL-2 and IL-15 induced the production of IL-17 and IFN-γ in a dose dependent manner by PBMCs.” elimination YH, ZX a negative regulation that one interactor eliminates another. eliminate, eliminated, eliminates, eliminating, abolish, abolished, abolishes, abolishing, abrogation bacterial conjugation YH 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. WEB: http://en.wikipedia.org/wiki/Bacterial_conjugation hydrogen binding WEB: http://www.ncbi.nlm.nih.gov/books/NBK22567/ YH Interaction leading to the formation of hydrogen bond between two molecules regulation of assembly regulated // assembly YH, AR, JH a regulation process where one gene product regulates an assembly process which forms an assembly having another gene product. human molecular control interaction a human molecular interaction where one molecule controls another molecule. YH gene expression express, expressed, expresses, expressing, expression, expressions a biological interaction that uses the information from a gene to synthesize a functional gene product. YH, ZX accessory regulation YH, ZX facilitate, facilitates, facilitating, faciliteted, help, helps, helped a positive regulation that one interactor facilitates a phenomenon such as a phenotype. This is an accessory effect not a major one. positive regulation of protein activity negative protein activity regulation a regulation of protein activitiy process that involves a positive regulation YH, AO positively regulated // activity, positively regulates // activity, dependent // stimulation host-pathogen interaction An interaction that involves a host (host organism or host cell) and pathogen organism at a specific condition. YH gene fusion 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 gene AND (fuse, fused, fuses, fusing) WEB: http://en.wikipedia.org/wiki/Gene_fusion host cell-pathogen interaction YH An host-pathogen interaction where the host is a cell. induction by binding to protein YH, AO, JH The Salmonella invasin SipB induces macrophage apoptosis by binding to caspase-1 induction ... by binding to // induces .. through binding// induced ... by binding to // caused ... by binding to // causes ... through ... binding an induction that is achieved by binding to a protein macrophage-pathogen interaction An host cell-pathogen interaction where the host cell is a macrophage. YH human molecular degradation YH protein heterodimerization heterodimerize, heterodimerized, heterodimerizes, heterodimerizing a protein dimerization where two proteins are different. YH, ZX protein homodimerization YH, ZX homodimerize, homodimerized, homodimerizes, homodimerizing a protein dimerization where two proteins are the same. macrophage-pathogen protein-protein interaction YH 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. macrophage-pathogen PPI overexpression increased gene expression a gene expression that has increased volume. overexpression YH, ZX hyper-expression, hyperactivate, hyperactivated, hyperactivates, hyperactivation, hyperexpression, overexpression hyperphosphorylation hyperphosphorylate, hyperphosphorylated, hyperphosphorylates, hyperphosphorylation YH, ZX immuno-precipitation immuno-precipitate, immuno-precipitated, immuno-precipitates, immuno-precipitating, immuno-precipitation, immunoprecipitate, immunoprecipitated, immunoprecipitates, immunoprecipitating, immunoprecipitation, immunopreticipate, immunopreticipated, immunopreticipates, immunopreticipating a translocation that one interactor is precipitated based on an immunological precipitation process. YH, ZX positive regulation YH, ZX YH: different types of positive regulations exist. These types are related to different qualities and phenotyes of regulated targets. positively regulate, positive regulations, positively regulated, positively regulating, promote, promoted, promotes, promoting impairment impair, impaired, impairing, impairs, cripple, crippled, cripples, crippling, sever, severed, severs YH, ZX A negative regulation that disables, damages, or impairs the functioning of another entity. inactivation inactivate, inactivated, inactivates, inactivating, inactivation YH, ZX a negative regulation that one interactor inactivates another. increase increase, increased, increases, increasing, augment, augmented, augmenting, augments, elavating, elevate, elevated, elevates, elevating, raise, raised, raises, raising, enhance, enhanced, enhances, enhancing, enhancement augmentation YH, ZX a positive regulation that leads to the increase of a quality of an entity. enhancement elavation human molecular synthesis induction induce, induced, induces, inducing, induction, trigger, triggered, triggering, triggerring, triggers, initiate, initiated, initiates, initiating, stimulate, stimulation, stimulated, stimulating, dependent // inducible leading a positive regulation that leads to the induction of a new interactor due to the presence of another interactor. triggering YH, ZX human molecular regulatory reaction inhibition YH, ZX a negative regulation that one interactor inhibites another. inhibit, inhibited, inhibiting, inhibition, inhibitor, inhibitors, inhibits, block, blocked, blocking, blocks input interactor YH an interactor that is an input of an interaction. interference interfere, interferes, interfered, interfering, perturb, perturbed, perturbing, perturbs, obstruction YH, ZX a negative regulation that one interactor interferes a process. human molecular modulation YH human template reaction regulation YH host gene mutant-pathogen interaction YH An host-pathogen interaction where the host is a gene mutant human molecular conversion YH a human molecular interaction where one molecule converts to another molecule. human molecular template reaction small molecule host An organism bearing a host role. positive regulator role an interactor role that is borne by a material entity that positively regulates an interaction. YH pathway step negative regulator role YH an interactor role that is borne by a material entity that negatively regulates an interaction. macrophage-pathogen PPI inducing cell death A macrophage-pathogen protein-protein interaction that induces cell death. The Salmonella invasin SipB induces macrophage apoptosis by binding to caspase-1. From: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC26795/ YH neutralization neutralise, neutralised, neutralises, neutralising, neutralize, neutralized, neutralizes, neutralizing YH, ZX a biochemical reaction that one interactor neutrolizes another. positive regulator YH an interaction regulator that positively regulates an interaction. oxidation oxidate, oxidated, oxidates, oxidating, oxidation, oxidise, oxidised, oxidises, oxidising, oxidize, oxidized, oxidizes, oxidizing YH, ZX an enzymatic reaction where a molecule gains oxygen. host-pathogen mutant interaction An host-pathogen interaction where the pathogen is a gene mutant YH negative regulator YH an interaction regulator that negatively regulates an interaction. deactivator role 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 macrophage-pathogen interaction YH An host cell-pathogen interaction where the host is a macrophage cell motivator role https://en.wikipedia.org/wiki/Motivation#Herzberg's_two-factor_theory Oliver He an input interactor role that is borne by a material entity that motivates a process. precedence YH, ZX an indirect association that one interactor is preceded by another interactor. precede, preceded, precedes, preceding prevention prevent, prevented, preventing, prevents YH, ZX hygiene factor role Oliver He 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. https://en.wikipedia.org/wiki/Motivation#Herzberg's_two-factor_theory output interactor an interactor that is an output of an interaction. YH epithelial cell-pathogen interaction YH An host cell-pathogen interaction where the host is an epithelial cell reactivation reactivate, reactivated, reactivates, reactivating, reactivation an activation that repeats. YH, ZX recruitment recruit, recruite, recruited, recruites, recruiting, recruits a positive regulation that leads the recruitment of one interactor from one location to another. YH, ZX epithelial cell-pathogen protein-protein interaction YH 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/ epithelial cell-pathogen PPI regulation 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 A regulation represents a regulatory interaction between two interactors. GO: GO_0065007 interaction network model https://en.wikipedia.org/wiki/Interactome An information content entity that models interaction network stabilization stabilization, stabilize, stabilized, stabilizes, stabilizing YH, ZX a postive interaction that one interactor increases the stability of another interactor. synergization 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 termination terminate, terminated, terminates, terminating YH, ZX a negative regulation that leads to a process termination. transactivation 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 a gene expression regulation that leads to an increased rate of gene expression triggered either by biological processes or by artificial means. gene transcription WEB: http://en.wikipedia.org/wiki/Transcription_%28genetics%29 transcribe, transcribed, transcribes, transcribing, transcription an interaction process that creates a complementary RNA copy of a sequence of DNA. YH genetic transduction a cell-cell interaction that transfers viral, bacterial, or both bacterial and viral DNA from one cell to another using a bacteriophage vector. transduce, transduced, transducer, transducers, transduces, transducing, transduction YH, ZX translocation translocation, transloated, translocating, translocates, migrated, migration, migrates migrating, mobilization, mobilize, mobilized, mobilizes, mobilizing, mobilisation, mobilise, mobilised, mobilises, mobilising A process that changes the location of a material entity. YH, ZX tyrosine-phosphorylation tyrosine-phosphorylated YH, ZX co-expression YH a correlation association that two genes are co-expressed in a system. deregulation YH a negative regulation that results in the deregulation of one interactor on a process. one-way interaction A one-way interaction is an interaction that shows one direction between interactors. YH export YH a translocation that one interactor exports from one location import YH a translocation that one interactor imports from one location secretion YH a translocation that one interactor secretes from the inside of another interactor protein-protein interaction YH, ZX an interaction between two proteins. gene-protein interaction an interaction that involves in a gene DNA and a protein YH, ZX acetylation reaction MI:0192 PSI-MI Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues. acetylation amidation reaction 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. MI:0193 PSI-MI amidation cleavage reaction Covalent bond breakage in a molecule leading to the formation of smaller molecules. MI:0194 PSI-MI cleavage covalent binding Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners. MI:0195 PSI-MI deacetylation reaction MI:0197 N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues. PSI-MI deacetylation defarnesylation reaction MI:0198 PSI-MI S-farnesyl-L-cysteined is cleaved and returns a C residue. defarnesylation deformylation reaction MI:0199 N6-formyl-L-lysine is cleaved and returns a K residue. PSI-MI deformylation degeranylation reaction MI:0200 PSI-MI S-geranylgeranyl-L-cysteine is cleaved and returns a C residue. degeranylation demyristoylation reaction MI:0201 N6-myristoyl-L-lysine is cleaved and returns a K residue. PSI-MI demyristoylation depalmitoylation reaction MI:0202 PSI-MI 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 dephosphorylation reaction MI:0203 PSI-MI Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues. dephosphorylation deubiquitination reaction Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins. MI:0204 PSI-MI deubiquitination farnesylation reaction MI:0206 PSI-MI Reversible reaction that can affect C residue. farnesylation formylation reaction MI:0207 PSI-MI Reaction that can affect K or G residues. Reside is functionalised with a formyl group. formylation genetic interaction MI:0208 PSI-MI geranylgeranylation reaction 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. MI:0209 PSI-MI geranylgeranylation hydroxylation reaction 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. MI:0210 PSI-MI hydroxylation lipid addition Covalent or non covalent binding of lipid group on a protein residue. MI:0211 PSI-MI lipid cleavage reaction Cleavage of a lipid group covalently bound to a protein residue. MI:0212 PSI-MI lipid cleavage methylation reaction MI:0213 PSI-MI 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 palmitoylation reaction Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues. MI:0216 PSI-MI palmitoylation ubiquitination reaction MI:0220 PSI-MI Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target. ubiquitination colocalization 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. MI:0403 PSI-MI direct interaction Interaction between molecules that are in direct contact with each other. MI:0407 PSI-MI disulfide bond Covalent bond mediated by 2 sulfur atoms. MI:0408 PSI-MI enzymatic reaction Biochemical reaction MI:0414 PSI-MI terms aiming to represent biochemical reactions referring to their resulting product modifications. transglutamination reaction Gln-Lys cross-link catalyzed by a transglutaminase. MI:0556 PSI-MI transglutamination adp ribosylation reaction Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues. MI:0557 PSI-MI adp ribosylation deglycosylation reaction MI:0558 PSI-MI Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins. deglycosylation glycosylation reaction MI:0559 PSI-MI 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 sumoylation reaction MI:0566 PSI-MI 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 neddylation reaction MI:0567 PSI-MI 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 desumoylation reaction Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins. MI:0568 PSI-MI desumoylation deneddylation reaction 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. MI:0569 PSI-MI deneddylation protein cleavage Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation. MI:0570 PSI-MI mrna cleavage Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner. MI:0571 PSI-MI dna cleavage Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments. MI:0572 PSI-MI dna strand elongation DNA replication elongation MI:0701 PSI-MI 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 elongation synthetic MI:0794 PSI-MI synthetic genetic interaction (sensu inequality) synthetic genetic interaction defined by inequality asynthetic MI:0795 PSI-MI asynthetic asynthetic genetic interaction (sensu inequality) suppression Alleviating interaction MI:0796 PSI-MI suppression suppressive genetic interaction (sensu inequality) epistasis MI:0797 PSI-MI epistatic epistatic genetic interaction (sensu inequality) phosphotransfer reaction MI:0844 PSI-MI Reaction where a phosphate is transferred between two proteins of a phosphorelay system. phosphotransfer demethylation reaction MI:0871 PSI-MI The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian. demethylation nucleoside triphosphatase reaction Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate. MI:0881 PSI-MI triphosphatase react atpase reaction Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate. MI:0882 PSI-MI gtpase reaction Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate. MI:0883 PSI-MI rna cleavage Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner. MI:0902 PSI-MI nucleic acid cleavage Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments. MI:0910 PSI-MI ncl acid cleavage association 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. MI:0914 PSI-MI physical association 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. MI:0915 PSI-MI noninteractive MI:0932 PSI-MI 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 negative genetic interaction MI:0933 PSI-MI negative gen int neutral genetic interaction MI:0934 PSI-MI neutral gent int positive genetic interaction MI:0935 PSI-MI positive gent int oxidoreductase activity electron transfer reaction 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. MI:0945 PSI-MI redox reaction phosphopantetheinylation 2009-10-28T01:20:40Z MI:0971 PSI-MI The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine. orchard p_patetheinylation deamination reaction 2010-04-26T10:49:06Z MI:0985 PSI-MI The removal of an amine group from a molecule. deamination orchard nucleic acid strand elongation reaction 2010-04-26T10:52:22Z MI:0986 PSI-MI The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase. orchard strand elongation rna strand elongation 2010-04-26T11:00:08Z MI:0987 PSI-MI 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 rna elongation diphtamidation reaction 2010-11-11T12:36:51Z A modification that converts an L-histidine residue to diphthamide. MI:1027 PSI-MI diphthamidation orchard predicted interaction 2011-08-03T11:14:11Z Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method. MI:1110 PSI-MI orchard predicted self interaction 2012-01-03T01:19:22Z Intra-molecular interaction between two or more regions of the same molecule. MI:1126 PSI-MI 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. orchard putative self interaction 2012-01-03T01:21:58Z 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. MI:1127 PSI-MI 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. orchard carboxylation reaction 2012-01-03T03:24:05Z Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins. MI:1139 PSI-MI carboxylation orchard decarboxylation reaction 2012-01-03T03:31:42Z 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). MI:1140 PSI-MI decarboxylation orchard aminoacylation reaction 2012-01-03T03:49:50Z Aminoacylation is the process of adding an aminoacyl group to a compound. MI:1143 PSI-MI aminoacylation orchard phospholipase reaction 2012-01-03T04:08:14Z MI:1146 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. PSI-MI orchard ampylation reaction 2012-01-03T04:21:12Z MI:1148 PSI-MI ampylation orchard uridylation reaction 2012-08-10T07:50:08Z MI:1230 PSI-MI The formation of a phosphodiester or phosphoramide ester of UMP and amino acid (MOD:01166). orchard umpylation uridylation proline isomerization reaction 2012-08-10T09:02:28Z MI:1237 PSI-MI The conversion between cis- and trans- peptide bonds formed by the amine group of a proline. orchard isomerase reaction 2012-08-10T12:51:00Z MI:1250 PSI-MI The catalysis of the structural rearrangement of isomers. orchard methylmalonyl-CoA isomerase reaction 2012-08-10T01:23:35Z MI:1251 PSI-MI 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 enhancement 2013-06-05T19:12:17Z <new synonym> Aggravating interaction MI:1271 PSI-MI orchard positive epistasis 2013-06-05T20:05:15Z MI:1272 PSI-MI orchard maximal epistasis 2013-06-05T20:11:27Z MI:1273 PSI-MI orchard minimal epistasis 2013-06-05T20:13:14Z MI:1274 PSI-MI orchard neutral epistasis 2013-06-05T20:22:53Z MI:1275 PSI-MI orchard opposing epistasis 2013-06-05T20:25:26Z MI:1276 PSI-MI orchard qualitative epistasis 2013-06-05T20:26:38Z MI:1277 PSI-MI orchard mutual enhancement 2013-06-05T20:31:30Z MI:1278 PSI-MI orchard unilateral enhancement 2013-06-05T20:33:13Z MI:1279 PSI-MI orchard mutual suppression 2013-06-05T20:35:53Z MI:1280 PSI-MI orchard mutual suppression (complete) 2013-06-05T20:37:41Z MI:1281 PSI-MI orchard mutual suppression (partial) 2013-06-05T20:39:12Z MI:1282 PSI-MI orchard suppression-enhancement 2013-06-05T20:43:52Z MI:1283 PSI-MI orchard quantitative epistasis 2013-06-05T20:47:35Z MI:1284 PSI-MI orchard opposing epistasis 2013-06-05T20:51:51Z MI:1285 PSI-MI orchard over-suppression 2013-06-05T21:04:18Z MI:1286 PSI-MI orchard mutual over-suppression 2013-06-05T21:06:09Z MI:1287 PSI-MI orchard over-suppression-enhancement 2013-06-05T21:11:03Z MI:1288 PSI-MI orchard phenotype bias 2013-06-05T21:15:34Z MI:1289 PSI-MI orchard suppression (complete) 2013-06-05T21:34:57Z MI:1290 PSI-MI orchard suppression (partial) 2013-06-05T21:36:07Z MI:1291 PSI-MI orchard unilateral suppression 2013-06-05T21:37:28Z MI:1292 PSI-MI orchard unilateral suppression (complete) 2013-06-05T21:38:36Z MI:1293 PSI-MI orchard unilateral suppression (partial) 2013-06-05T21:39:32Z MI:1294 PSI-MI orchard unilateral over-suppression 2013-06-05T21:54:08Z MI:1295 PSI-MI orchard de-ADP-ribosylation reaction 2013-06-06T10:34:18Z MI:1310 Measure of hydrolytic reactions that release ADP-ribose. PSI-MI mono-ADP-ribosylhydrolase reaction orchard sulfurtransfer reaction 2014-01-08T11:16:12Z MI:1327 PSI-MI Reaction where a sulfate group is transferred between two proteins orchard sulfurtransfer sulphurtransfer reaction gene 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/ protein classic metabolic pathway PW:0000002 The definition was compiled based on a number of available defintions in various dictionaries. The various, enzyme controlled, series of reactions allowing for the conversion of materials, energy availability and biodegradation of xenobiotics. pathway signaling pathway PW:0000003 The definition was compiled based on a number of definitions available in various dictionaries. 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 regulatory pathway PW:0000004 The definition was complied based on a number of definitions available in several dictionaries 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 disease pathway 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. PW:0000013 complex human diseases pathway drug pathway 2010-03-15T11:01:15Z PW:0000754 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 pathway DNA RNA ready for release pending final vetting requires discussion axiom holds for all times ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation https://github.com/oborel/obo-relations/ Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] OBO Relations Ontology The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.