2015-12-10 He Zhang Alan Ruttenberg Alan Ruttenberg Harrison Strachan Jingshan Huang Asiyah Yu Lin This is the release of December 12, 2015. It will always be available at http://purl.obolibrary.org/ncro/2015-12-10/ncro.owl. While current, this ontology is also available at http://purl.obolibrary.org/obo/ncro.owl This file is a merge of NCRO and any imported ontologies or terms. You can access the ontology that existed before the merge, with imports intact, at http://purl.obolibrary.org/obo/ncro/YYYY-MM-DD/ncro.owl or, for the current version, http://purl.obolibrary.org/obo/ncro/prebuild/ncro.owl This ontology is currently undergoing changes. ID deprecation policies will start in the next couple of months. In the mean time, identifiers may be deleted and not marked obsolete. d 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 editor preferred label 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 label editor preferred term example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober example example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status OBI_0000281 PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status 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. definition 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 editor note IAO:0000116 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. 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 has obsolescence reason PERSON:Alan Ruttenberg PERSON:Melanie Courtot Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note is denotator type Alan Ruttenberg In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') relates an class defined in an ontology, to the type of it's denotator is denotator type imported from For external terms/classes, the ontology from which the term was imported GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Alan Ruttenberg PERSON:Melanie Courtot imported from expand expression to Chris Mungall A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" expand expression to expand assertion to A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property antisymmetric property Alan Ruttenberg antisymmetric property part_of antisymmetric property xsd:true use boolean value xsd:true to indicate that the property is an antisymmetric property OBO foundry unique label The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . An alternative name for a class or property which is unique across the OBO Foundry. GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot has ID digit count Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Person:Alan Ruttenberg has ID range allocated to Person:Alan Ruttenberg Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID prefix Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" 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) An axiom associated with a term expressed using natural language Person:Alan Ruttenberg 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) is allocated id range Add as annotation triples in the granting ontology PERSON:Alan Ruttenberg Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" is allocated id range has axiom label A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI Person:Alan Ruttenberg Person:Alan Ruttenberg has axiom id term replaced by Add as annotation triples in the granting ontology Person:Alan Ruttenberg Person:Alan Ruttenberg Use on obsolete terms, relating the term to another term that can be used as a substitute term replaced by part of a core relation that holds between a part and its whole part_of preceded by is 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 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. occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in is_about_grouped_miRNA 2015-05-16T19:28:03Z He_Zhang is_about_miRNA is_about_miRNA_target_gene is_classified_into_gene_family_group 2015-05-16T19:27:05Z He_Zhang is_gene_template_of_mRNA is_model_of_disease is_predicted_target_of 2015-05-17T07:52:46Z He_Zhang miRNA_expressed_in_tissue regulate_miRNA_transcription regulate_mRNA_translation has_predicted_target 2015-05-17T07:51:13Z participates in a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in has participant a relation between a process and a continuant, in which the continuant is somehow involved in the process has_participant derives from a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity derives_from regulates GO x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y David Hill Tanya Berardini Chris Mungall negatively regulates Chris Mungall x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y positively regulates Chris Mungall x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y member of is member of SIO is member of is a mereological relation between a item and a collection. member part of has member SIO has member is a mereological relation between a collection and an item. in similarity relationship with ECO:0000041 Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. SO:similar_to sameness similar to in homology relationship with Similarity that results from common evolutionary origin. homologous to in non functional homology relationship with SO:non_functional_homolog_of Structural homology that involves a pseudogenic feature and its functional ancestor. non functional homologous to entity entity Entity An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf Julius Caesar Verdi’s Requiem the Second World War your body mass index 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 per discussion with Barry Smith 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 y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] 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]) 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]) (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] 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]) 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]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] 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 (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] 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]) (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] 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] 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 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]) occurrent Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] 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. per discussion with Barry Smith 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. 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]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [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] (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ic (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) 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 (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] 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]) 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]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] 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]) (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] spatial region (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) s-region SpatialRegion (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) temporal region (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] 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 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]) 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]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] per discussion with Barry Smith 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 two-dimensional spatial region 2d-s-region TwoDimensionalSpatialRegion (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) an infinitely thin plane in space. the surface of a sphere-shaped part of space (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) spatiotemporal region (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) st-region (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] SpatiotemporalRegion (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) 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] 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. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] 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] 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] 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 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 If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] 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]) 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] 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 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]) (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] All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] zero-dimensional spatial region 0d-s-region ZeroDimensionalSpatialRegion (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) 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 (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] (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] 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]) 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]) 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] 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 (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] 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]) per discussion with Barry Smith 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. role 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 (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] 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]) fiat object part BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions fiat-object-part FiatObjectPart (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] one-dimensional spatial region (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] OneDimensionalSpatialRegion 1d-s-region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) an edge of a cube-shaped portion of space. (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) object aggregate ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ObjectAggregate object-aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects three-dimensional spatial region ThreeDimensionalSpatialRegion 3d-s-region (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] 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) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] 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 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]) 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. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function 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. 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 A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] process boundary (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] p-boundary ProcessBoundary Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) the boundary between the 2nd and 3rd year of your life. Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) 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. A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] 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 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]) MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic 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 (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) (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] A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) continuant fiat boundary cf-boundary ContinuantFiatBoundary (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) 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 one-dimensional continuant fiat boundary OneDimensionalContinuantFiatBoundary (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] 1d-cf-boundary The Equator a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] process profile process-profile (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. ProcessProfile The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] relational quality r-quality (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] 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. RelationalQuality a marriage bond, an instance of love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) two-dimensional continuant fiat boundary (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] TwoDimensionalContinuantFiatBoundary 2d-cf-boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) zero-dimensional continuant fiat boundary (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] requested by Melanie Courtot zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. 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. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] history history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) transfer RNA A single-stranded RNA molecule containing about 70-90 nucleotides, folded by intrastrand base pairing into a characteristic secondary ('cloverleaf') structure that carries a specific amino acid and matches it to its corresponding codon on an mRNA during protein synthesis. ChemIDplus:9014-25-9 KEGG COMPOUND:C00066 transfer RNA tRNA ribosomal RNA KEGG COMPOUND:C00240 RNA molecules which are essential structural and functional components of ribosomes, the subcellular units responsible for protein synthesis. Ribosomal RNA ribosomal RNA rRNA molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity organic group Any substituent group or skeleton containing carbon. ribonucleic acid ChemIDplus:63231-63-0 High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. ribonucleic acid ribonucleic acids RNA amino-acid residue When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue. amino-acid residue small nuclear RNA A class of small RNA molecules which are comprised of approximately 150 nucleotides and which are found within the nucleus of eukaryotic cells. CiteXplore:22907602 CiteXplore:23070852 CiteXplore:23190533 CiteXplore:23348838 CiteXplore:23394998 CiteXplore:23426875 CiteXplore:23727230 CiteXplore:23740936 Wikipedia:Small_nuclear_RNA snRNA RNA(circular) KEGG COMPOUND:C02073 RNA(circular) circRNA cell line MB, SS, JZ, MAH, BP, CS, YH disease of cellular proliferation A disease that is characterized by abnormally rapid cell division. cell process disease cancer A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. ICD10CM:C80 ICD10CM:C80.1 ICD9CM:199 MSH:D009369 NCI:C9305 SNOMEDCT_US_2015_03_01:154432008 SNOMEDCT_US_2015_03_01:154433003 SNOMEDCT_US_2015_03_01:154577008 SNOMEDCT_US_2015_03_01:187597000 SNOMEDCT_US_2015_03_01:188475001 SNOMEDCT_US_2015_03_01:188482002 SNOMEDCT_US_2015_03_01:190150006 SNOMEDCT_US_2015_03_01:269513004 SNOMEDCT_US_2015_03_01:269623003 SNOMEDCT_US_2015_03_01:269626006 SNOMEDCT_US_2015_03_01:269634000 SNOMEDCT_US_2015_03_01:363346000 SNOMEDCT_US_2015_03_01:38807002 UMLS_CUI:C0006826 malignant neoplasm malignant tumor primary cancer disease A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. MSH:D004194 NCI:C2991 SNOMEDCT_US_2015_03_01:64572001 UMLS_CUI:C0012634 negative regulation of transcription from RNA polymerase II promoter Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter. down regulation of transcription from RNA polymerase II promoter down-regulation of transcription from RNA polymerase II promoter downregulation of transcription from RNA polymerase II promoter inhibition of transcription from RNA polymerase II promoter negative regulation of transcription from Pol II promoter 3'-5'-exoribonuclease activity 3'-5' exoribonuclease activity Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule. EC:3.1.13.- Reactome:REACT_102966 Reactome:REACT_108214 Reactome:REACT_20588 Reactome:REACT_33991 Reactome:REACT_34078 Reactome:REACT_78363 Reactome:REACT_82118 Reactome:REACT_88115 Reactome:REACT_89880 Reactome:REACT_92153 Reactome:REACT_93499 Reactome:REACT_95913 Reactome:REACT_95921 Reactome:REACT_96267 Reactome:REACT_99422 molecular_function Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. molecular function RNA binding Interacting selectively and non-covalently with an RNA molecule or a portion thereof. Reactome:REACT_101703 Reactome:REACT_103323 Reactome:REACT_106430 Reactome:REACT_107757 Reactome:REACT_108232 Reactome:REACT_108368 Reactome:REACT_109723 Reactome:REACT_12458 Reactome:REACT_29965 Reactome:REACT_77167 Reactome:REACT_78197 Reactome:REACT_87164 Reactome:REACT_89329 Reactome:REACT_90531 Reactome:REACT_98683 catalytic activity Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. Wikipedia:Enzyme enzyme activity nuclease activity Catalysis of the hydrolysis of ester linkages within nucleic acids. EC:3.1.-.- endonuclease activity Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks. Reactome:REACT_100654 Reactome:REACT_101397 Reactome:REACT_103600 Reactome:REACT_106502 Reactome:REACT_108614 Reactome:REACT_110731 Reactome:REACT_112366 Reactome:REACT_1124 Reactome:REACT_112509 Reactome:REACT_112615 Reactome:REACT_112782 Reactome:REACT_113127 Reactome:REACT_113480 Reactome:REACT_113819 Reactome:REACT_114931 Reactome:REACT_115221 Reactome:REACT_115226 Reactome:REACT_115382 Reactome:REACT_115937 Reactome:REACT_116011 Reactome:REACT_1914 Reactome:REACT_34610 Reactome:REACT_6746 Reactome:REACT_6774 Reactome:REACT_77706 Reactome:REACT_78624 Reactome:REACT_79198 Reactome:REACT_80387 Reactome:REACT_80628 Reactome:REACT_80681 Reactome:REACT_80797 Reactome:REACT_81714 Reactome:REACT_87541 Reactome:REACT_89800 Reactome:REACT_90034 Reactome:REACT_90935 Reactome:REACT_92894 endoribonuclease activity Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks. Reactome:REACT_22313 Reactome:REACT_75787 exonuclease activity Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end. exoribonuclease activity Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of an RNA molecule. Reactome:REACT_109605 Reactome:REACT_109680 Reactome:REACT_20556 Reactome:REACT_29104 Reactome:REACT_32104 Reactome:REACT_78260 Reactome:REACT_79364 Reactome:REACT_79874 Reactome:REACT_87278 Reactome:REACT_88925 Reactome:REACT_90233 Reactome:REACT_94168 Reactome:REACT_99687 Reactome:REACT_99790 ribonuclease activity Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. transporter activity Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. Reactome:REACT_6315 binding The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. Wikipedia:Binding_(molecular) cellular_component NIF_Subcellular:sao-1337158144 NIF_Subcellular:sao1337158144 The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. cell or subcellular entity cellular component intracellular The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. Wikipedia:Intracellular internal to cell protoplasm cell NIF_Subcellular:sao1813327414 The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. Wikipedia:Cell_(biology) nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus nucleoplasm NIF_Subcellular:sao661522542 That part of the nuclear content other than the chromosomes or the nucleolus. Wikipedia:Nucleoplasm cytoplasm All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. Wikipedia:Cytoplasm nucleobase-containing compound metabolic process Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism nucleobase, nucleoside, nucleotide and nucleic acid metabolism transcription, DNA-templated DNA-dependent transcription The cellular synthesis of RNA on a template of DNA. Wikipedia:Transcription_(genetics) cellular transcription, DNA-dependent transcription, DNA-dependent regulation of transcription, DNA-templated Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. regulation of cellular transcription, DNA-dependent regulation of transcription, DNA-dependent regulation of transcription from RNA polymerase II promoter Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter. regulation of transcription from Pol II promoter mRNA cleavage Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner. RNA processing Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. Wikipedia:Post-transcriptional_modification mRNA processing Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide. Reactome:REACT_100203 Reactome:REACT_107308 Reactome:REACT_109953 Reactome:REACT_113864 Reactome:REACT_114358 Reactome:REACT_115262 Reactome:REACT_1768 Reactome:REACT_32742 Reactome:REACT_33642 Reactome:REACT_82691 Reactome:REACT_90366 Reactome:REACT_91511 Reactome:REACT_93186 Reactome:REACT_94083 Reactome:REACT_96661 Reactome:REACT_97412 Reactome:REACT_97436 RNA catabolic process RNA breakdown RNA catabolism RNA degradation The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. RNA localization A process in which RNA is transported to, or maintained in, a specific location. RNA localisation establishment and maintenance of RNA localization RNA export from nucleus RNA export from cell nucleus RNA export out of nucleus RNA transport from nucleus to cytoplasm RNA-nucleus export Reactome:REACT_1004 Reactome:REACT_104043 Reactome:REACT_108003 Reactome:REACT_114184 Reactome:REACT_1334 Reactome:REACT_29222 Reactome:REACT_30837 Reactome:REACT_30884 Reactome:REACT_53 Reactome:REACT_78063 Reactome:REACT_80132 Reactome:REACT_80198 Reactome:REACT_80579 Reactome:REACT_81658 Reactome:REACT_82156 Reactome:REACT_82661 Reactome:REACT_84373 Reactome:REACT_84418 Reactome:REACT_85495 Reactome:REACT_86488 Reactome:REACT_87758 Reactome:REACT_89603 Reactome:REACT_904 Reactome:REACT_90560 Reactome:REACT_91473 Reactome:REACT_92226 Reactome:REACT_95332 Reactome:REACT_98342 Reactome:REACT_99708 The directed movement of RNA from the nucleus to the cytoplasm. translation Reactome:REACT_100338 Reactome:REACT_100851 Reactome:REACT_101045 Reactome:REACT_101324 Reactome:REACT_1014 Reactome:REACT_103420 Reactome:REACT_105544 Reactome:REACT_29980 Reactome:REACT_33559 Reactome:REACT_77710 Reactome:REACT_79784 Reactome:REACT_81734 Reactome:REACT_81833 Reactome:REACT_82171 Reactome:REACT_83429 Reactome:REACT_83530 Reactome:REACT_86996 Reactome:REACT_95535 Reactome:REACT_96394 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis protein biosynthetic process protein formation protein synthesis protein translation translational elongation Reactome:REACT_100207 Reactome:REACT_100561 Reactome:REACT_101290 Reactome:REACT_101737 Reactome:REACT_102082 Reactome:REACT_103580 Reactome:REACT_108124 Reactome:REACT_108677 Reactome:REACT_108858 Reactome:REACT_1477 Reactome:REACT_30678 Reactome:REACT_31079 Reactome:REACT_80015 Reactome:REACT_80831 Reactome:REACT_81624 Reactome:REACT_82124 Reactome:REACT_88049 Reactome:REACT_93503 Reactome:REACT_96070 The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. translation elongation regulation of translation Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. regulation of protein anabolism regulation of protein biosynthesis regulation of protein formation regulation of protein synthesis cellular aromatic compound metabolic process The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. aromatic compound metabolism transport The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. 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. Wikipedia:Biological_process biological process physiological process metabolic process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. Wikipedia:Metabolism metabolism catabolic process The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. Wikipedia:Catabolism breakdown catabolism degradation macromolecule catabolic process The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biopolymer catabolic process macromolecule breakdown macromolecule catabolism macromolecule degradation biosynthetic process The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. Wikipedia:Anabolism anabolism biosynthesis formation synthesis macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis macromolecule formation macromolecule synthesis RNA modification The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically. Wikipedia:RNA_editing regulation of biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. regulation of anabolism regulation of biosynthesis regulation of formation regulation of synthesis negative regulation of biosynthetic process Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. down regulation of biosynthetic process down-regulation of biosynthetic process downregulation of biosynthetic process negative regulation of anabolism negative regulation of biosynthesis negative regulation of formation negative regulation of synthesis positive regulation of biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. positive regulation of anabolism positive regulation of biosynthesis positive regulation of formation positive regulation of synthesis up regulation of biosynthetic process up-regulation of biosynthetic process upregulation of biosynthetic process negative regulation of metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. down regulation of metabolic process down-regulation of metabolic process downregulation of metabolic process negative regulation of metabolism positive regulation of metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. positive regulation of metabolism up regulation of metabolic process up-regulation of metabolic process upregulation of metabolic process regulation of catabolic process Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. regulation of breakdown regulation of catabolism regulation of degradation negative regulation of catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. down regulation of catabolic process down-regulation of catabolic process downregulation of catabolic process negative regulation of breakdown negative regulation of catabolism negative regulation of degradation positive regulation of catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. positive regulation of breakdown positive regulation of catabolism positive regulation of degradation up regulation of catabolic process up-regulation of catabolic process upregulation of catabolic process cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. cell physiology cellular physiological process response to organic substance Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus. production of ta-siRNAs involved in RNA interference Cleavage of double-stranded RNA to form trans-acting small interfering RNA molecules (siRNAs) of 21-23 nucleotides. ta-siRNAs arise from PolII genes and function like miRNAs to guide cleavage of target mRNAs. RNA interference, production of ta-siRNAs nuclear dicing body A small round nuclear body, measuring 0.2-0.8 microns in diameter that is diffusely distributed throughout the nucleoplasm. Several proteins known to be involved in miRNA processing have been localized to these structures. D-bodies are thought to be involved in primary-miRNA processing and/or storage/assembly of miRNA processing complexes. D body gene expression Reactome:REACT_100537 Reactome:REACT_101147 Reactome:REACT_101952 Reactome:REACT_105649 Reactome:REACT_108313 Reactome:REACT_29068 Reactome:REACT_34240 Reactome:REACT_71 Reactome:REACT_78136 Reactome:REACT_78959 Reactome:REACT_79662 Reactome:REACT_85241 Reactome:REACT_85359 Reactome:REACT_86357 Reactome:REACT_89816 Reactome:REACT_91657 Reactome:REACT_91965 Reactome:REACT_93586 Reactome:REACT_93968 Reactome:REACT_94814 Reactome:REACT_98256 The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. Wikipedia:Gene_expression regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. Wikipedia:Regulation_of_gene_expression regulation of macromolecule biosynthetic process Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. positive regulation of macromolecule biosynthetic process Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. negative regulation of macromolecule biosynthetic process Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. miRNA metabolic process The chemical reactions and pathways involving miRNA, microRNA, a class of single-stranded RNA molecules of about 21-23 nucleotides in length, which regulates gene expression. microRNA metabolic process miRNA catabolic process The chemical reactions and pathways resulting in the breakdown of miRNA, microRNA, a class of single-stranded RNA molecules of about 21-23 nucleotides in length, which regulates gene expression. microRNA catabolic process positive regulation of macromolecule metabolic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. negative regulation of macromolecule metabolic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. posttranscriptional regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript. positive regulation of gene expression Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. negative regulation of gene expression Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. response to organic cyclic compound Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus. response to organic cyclic substance cellular component organization A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. cell organisation cellular component organisation at cellular level cellular component organisation in other organism cellular component organization at cellular level cellular component organization in other organism RNA metabolic process RNA metabolism Reactome:REACT_107259 Reactome:REACT_107652 Reactome:REACT_110289 Reactome:REACT_21257 Reactome:REACT_30579 Reactome:REACT_31367 Reactome:REACT_33720 Reactome:REACT_80071 Reactome:REACT_83630 Reactome:REACT_84169 Reactome:REACT_85788 Reactome:REACT_88316 Reactome:REACT_89992 Reactome:REACT_91556 Reactome:REACT_92152 Reactome:REACT_94876 Reactome:REACT_99403 Reactome:REACT_99885 The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. RNA interference RNAi The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes. Wikipedia:RNA_interference posttranscriptional gene silencing by siRNA posttranscriptional gene silencing PTGS The inactivation of gene expression by a posttranscriptional mechanism. Wikipedia:Post_transcriptional_gene_silencing post-transcriptional gene silencing quelling RISC complex A ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation. RNA-induced silencing complex Wikipedia:RNA-induced_silencing_complex gene silencing Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, postranscriptional repression of gene expression. Wikipedia:Gene_silencing endoribonuclease activity, producing 5'-phosphomonoesters Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters. EC:3.1.26 exoribonuclease activity, producing 5'-phosphomonoesters Catalysis of the hydrolysis of ester linkages within ribonucleic acids by removing nucleotide residues from the 3' or 5' end to yield 5' phosphomonoesters. EC:3.1.13 Reactome:REACT_109371 Reactome:REACT_20560 Reactome:REACT_81094 Reactome:REACT_89209 Reactome:REACT_90720 Reactome:REACT_92855 Reactome:REACT_93863 Reactome:REACT_97640 Reactome:REACT_98936 exoribonuclease activity, producing 5' phosphomonoesters negative regulation of translation Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. down regulation of protein biosynthetic process down-regulation of protein biosynthetic process downregulation of protein biosynthetic process negative regulation of protein anabolism negative regulation of protein biosynthesis negative regulation of protein biosynthetic process negative regulation of protein formation negative regulation of protein synthesis heterocycle biosynthetic process The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle anabolism heterocycle biosynthesis heterocycle formation heterocycle synthesis regulation of nucleobase-containing compound metabolic process Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. regulation of metabolism aromatic compound biosynthetic process The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring. aromatic compound anabolism aromatic compound biosynthesis aromatic compound formation aromatic compound synthesis aromatic compound catabolic process The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring. aromatic compound breakdown aromatic compound catabolism aromatic compound degradation protein metabolic process The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification. Wikipedia:Protein_metabolism protein metabolic process and modification protein metabolism protein metabolism and modification ribonucleoprotein complex biogenesis A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex. RNA-protein complex biogenesis ribonucleoprotein complex biogenesis and assembly ribonucleoprotein complex assembly RNA-protein complex assembly RNP complex assembly The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. protein-RNA complex assembly production of siRNA involved in RNA interference Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference. RNA interference, production of guide RNAs RNA interference, production of siRNA production of guide RNAs involved in RNA interference ribonucleoprotein complex A macromolecular complex containing both protein and RNA molecules. RNA-protein complex RNP Wikipedia:Ribonucleoprotein protein-RNA complex ribonucleoprotein dsRNA fragmentation Cleavage of double-stranded RNA molecules by an RNaseIII-family enzyme to produce small RNAs (generally 20-30 nucleotides, depending on species) with biological function. double-stranded RNA fragmentation primary miRNA processing Any process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule. pri-miRNA processing primary microRNA processing pre-miRNA processing Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule. pre-microRNA processing regulation of cellular metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. regulation of cellular metabolism negative regulation of cellular metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. down regulation of cellular metabolic process down-regulation of cellular metabolic process downregulation of cellular metabolic process negative regulation of cellular metabolism positive regulation of cellular metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. Reactome:REACT_101225 Reactome:REACT_102187 Reactome:REACT_102331 Reactome:REACT_105293 Reactome:REACT_108571 Reactome:REACT_109170 Reactome:REACT_2122 Reactome:REACT_28360 Reactome:REACT_31270 Reactome:REACT_79603 Reactome:REACT_80902 Reactome:REACT_83058 Reactome:REACT_84314 Reactome:REACT_86633 Reactome:REACT_87840 Reactome:REACT_88060 Reactome:REACT_91293 Reactome:REACT_91429 Reactome:REACT_91906 Reactome:REACT_92487 Reactome:REACT_99393 positive regulation of cellular metabolism up regulation of cellular metabolic process up-regulation of cellular metabolic process upregulation of cellular metabolic process regulation of cellular biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. regulation of cellular anabolism regulation of cellular biosynthesis regulation of cellular formation regulation of cellular synthesis negative regulation of cellular biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. down regulation of cellular biosynthetic process down-regulation of cellular biosynthetic process downregulation of cellular biosynthetic process negative regulation of cellular anabolism negative regulation of cellular biosynthesis negative regulation of cellular formation negative regulation of cellular synthesis positive regulation of cellular biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. positive regulation of cellular anabolism positive regulation of cellular biosynthesis positive regulation of cellular formation positive regulation of cellular synthesis up regulation of cellular biosynthetic process up-regulation of cellular biosynthetic process upregulation of cellular biosynthetic process regulation of cellular catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. regulation of cellular breakdown regulation of cellular catabolism regulation of cellular degradation negative regulation of cellular catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. down regulation of cellular catabolic process down-regulation of cellular catabolic process downregulation of cellular catabolic process negative regulation of cellular breakdown negative regulation of cellular catabolism negative regulation of cellular degradation positive regulation of cellular catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. positive regulation of cellular breakdown positive regulation of cellular catabolism positive regulation of cellular degradation up regulation of cellular catabolic process up-regulation of cellular catabolic process upregulation of cellular catabolic process nuclear lumen The volume enclosed by the nuclear inner membrane. regulation of cellular protein metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell. regulation of cellular protein metabolism negative regulation of cellular protein metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell. down regulation of cellular protein metabolic process down-regulation of cellular protein metabolic process downregulation of cellular protein metabolic process negative regulation of cellular protein metabolism RNA biosynthetic process RNA anabolism RNA biosynthesis RNA formation RNA synthesis The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication. macromolecular complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together. macromolecule complex chromatoid body A ribonucleoprotein complex found in the cytoplasm of male germ cells, composed of exceedingly thin filaments that are consolidated into a compact mass or into dense strands of varying thickness that branch to form an irregular network. Contains mRNAs, miRNAs, and protein components involved in miRNA processing (such as Argonaute proteins and the endonuclease Dicer) and in RNA decay (such as the decapping enzyme DCP1a and GW182). ncRNA processing Any process that results in the conversion of one or more primary non-coding RNA (ncRNA) transcripts into one or more mature ncRNA molecules. cellular nitrogen compound metabolic process Reactome:REACT_102000 Reactome:REACT_103710 Reactome:REACT_107293 Reactome:REACT_108179 Reactome:REACT_109042 Reactome:REACT_13 Reactome:REACT_28699 Reactome:REACT_29108 Reactome:REACT_32429 Reactome:REACT_33347 Reactome:REACT_34326 Reactome:REACT_55564 Reactome:REACT_77741 Reactome:REACT_82379 Reactome:REACT_86268 Reactome:REACT_90299 Reactome:REACT_91959 Reactome:REACT_93580 Reactome:REACT_95666 Reactome:REACT_98086 Reactome:REACT_99241 The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. cellular nitrogen compound metabolism cellular macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells. cellular biopolymer biosynthetic process cellular macromolecule anabolism cellular macromolecule biosynthesis cellular macromolecule formation cellular macromolecule synthesis nucleobase-containing compound biosynthetic process The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids. nucleobase, nucleoside, nucleotide and nucleic acid anabolism nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis nucleobase, nucleoside, nucleotide and nucleic acid formation nucleobase-containing compound catabolic process The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. nucleobase, nucleoside, nucleotide and nucleic acid breakdown nucleobase, nucleoside, nucleotide and nucleic acid catabolism nucleobase, nucleoside, nucleotide and nucleic acid degradation ncRNA metabolic process Reactome:REACT_104424 Reactome:REACT_107260 Reactome:REACT_11052 Reactome:REACT_31743 Reactome:REACT_34395 Reactome:REACT_77416 Reactome:REACT_82057 Reactome:REACT_87487 Reactome:REACT_91823 Reactome:REACT_92649 Reactome:REACT_94145 The chemical reactions and pathways involving non-coding RNA transcripts (ncRNAs). ncRNA metabolism ncRNA catabolic process The chemical reactions and pathways resulting in the breakdown of non-coding RNA transcripts (ncRNAs). Includes the breakdown of cryptic unstable transcripts (CUTs). ncRNA breakdown ncRNA catabolism ncRNA degradation micro-ribonucleoprotein complex A complex containing both protein and micro-RNA (miRNA) molecules. miRNAs are approximately 22 nucleotide noncoding RNAs derived from endogenous genes; they are processed from the stem of a longer hairpin like structure termed a pre-miRNA. miRNP complex posttranscriptional gene silencing by RNA Any process of posttranscriptional gene inactivation (silencing) mediated by small RNA molecules that may trigger mRNA degradation or negatively regulate translation. RNA-mediated posttranscriptional gene silencing gene silencing by miRNA Downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: endolytic cleavage of mRNA cleavage or translational repression, usually accompanied by poly-A tail shortgening and subsequent degredation of the mRNA. gene silencing by microRNA miRNA-mediated gene silencing microRNA-mediated gene silencing production of miRNAs involved in gene silencing by miRNA Cleavage of stem-loop RNA precursors into microRNAs (miRNAs), a class of small RNAs that primarily silence genes by blocking the translation of mRNA transcripts into protein. gene silencing by miRNA, production of miRNAs miRNA processing miRNA-mediated gene silencing, production of miRNAs microRNA-mediated gene silencing, production of microRNAs production of microRNAs involved in gene silencing by microRNA miRNA binding Interacting selectively and non-covalently with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes. microRNA binding negative regulation of translation involved in gene silencing by miRNA The process in which microRNAs (miRNAs) block the translation of target mRNAs into proteins. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA will typically repress translation if the miRNA imperfectly base-pairs with the 3' untranslated regions of target mRNAs. down regulation of translation involved in gene silencing by miRNA down-regulation of translation involved in gene silencing by miRNA downregulation of translation involved in gene silencing by miRNA gene silencing by miRNA, negative regulation of translation negative regulation of translation involved in gene silencing by microRNA mRNA cleavage involved in gene silencing by miRNA The process in which microRNAs (miRNAs) direct the cleavage of target mRNAs. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA base pairing with near-perfect complementarity to the target mRNA will typically direct targeted endonucleolytic cleavage of the mRNA. Many plant miRNAs downregulate gene expression through this mechanism. gene silencing by miRNA, mRNA cleavage mRNA cleavage involved in gene silencing by microRNA miRNA-mediated gene silencing, mRNA cleavage miRNA loading onto RISC involved in gene silencing by miRNA The transfer of a microRNA (miRNA) strand from a miRNA:miRNA duplex onto the RNA-initiated silencing complex (RISC). gene silencing by miRNA, miRNA loading onto RISC miRNA-mediated gene silencing, miRNA loading onto RISC microRNA loading onto RISC involved in gene silencing by microRNA pre-miRNA export from nucleus Transport of pre-microRNAs (pre-miRNAs) from the nucleus to the cytoplasm. Pre-miRNAs are a ~60-70 nucleotide stem loop intermediate in miRNA production, produced by the nuclear cleavage of a primary miRNA (pri-mRNA) transcript. Pre-miRNAs are transported from the nucleus to the cytoplasm where further cleavage occurs to produce a mature miRNA product. pre-microRNA export from cell nucleus pre-microRNA export out of nucleus pre-microRNA transport from nucleus to cytoplasm pre-microRNA-nucleus export ribonucleoprotein granule A non-membranous macromolecular complex containing proteins and translationally silenced mRNAs. RNA granules contain proteins that control the localization, stability, and translation of their RNA cargo. Different types of RNA granules (RGs) exist, depending on the cell type and cellular conditions. RNP granule mRNP granule cytoplasmic ribonucleoprotein granule A ribonucleoprotein granule located in the cytoplasm. negative regulation of translation, ncRNA-mediated Any process, mediated by small non-coding RNAs, that stops, prevents or reduces the rate that mRNAs are effectively translated into protein. down regulation of mRNA translation, ncRNA-mediated down-regulation of mRNA translation, ncRNA-mediated downregulation of mRNA translation, ncRNA-mediated response to chemical Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. response to chemical stimulus response to chemical substance macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biopolymer metabolic process macromolecule metabolism organelle NIF_Subcellular:sao1539965131 Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. Wikipedia:Organelle intracellular organelle Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. intracellular membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. intracellular membrane-enclosed organelle intracellular non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. intracellular non-membrane-enclosed organelle organelle lumen The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. response to dsRNA Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a double-stranded RNA stimulus. response to double-stranded RNA ncRNA 3'-end processing Any process involved in forming the mature 3' end of a non-coding RNA molecule. ncRNA 3' end processing macromolecular complex subunit organization Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a macromolecular complex. cellular macromolecular complex organization cellular macromolecular complex subunit organisation cellular macromolecular complex subunit organization macromolecular complex organization macromolecular complex subunit organisation cellular metabolic process The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolism primary metabolic process The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. primary metabolism cellular catabolic process The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. cellular breakdown cellular catabolism cellular degradation cellular biosynthetic process The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. cellular anabolism cellular biosynthesis cellular formation cellular synthesis cellular macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells. cellular biopolymer metabolic process cellular macromolecule metabolism cellular macromolecule catabolic process The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells. cellular biopolymer catabolic process cellular macromolecule breakdown cellular macromolecule catabolism cellular macromolecule degradation cellular protein metabolic process Reactome:REACT_101554 Reactome:REACT_102155 Reactome:REACT_105825 Reactome:REACT_106151 Reactome:REACT_108005 Reactome:REACT_109022 Reactome:REACT_17015 Reactome:REACT_32904 Reactome:REACT_34473 Reactome:REACT_80561 Reactome:REACT_81994 Reactome:REACT_82523 Reactome:REACT_85873 Reactome:REACT_86658 Reactome:REACT_89852 Reactome:REACT_91052 Reactome:REACT_93132 Reactome:REACT_96466 Reactome:REACT_99179 The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification. cellular protein metabolism cellular nitrogen compound catabolic process The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. cellular nitrogen compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. organelle part Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane. intracellular part Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. nuclear part Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. NIF_Subcellular:sao1499850686 nuclear subcomponent nucleus component cytoplasmic part Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. cytoplasm component intracellular organelle part A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane. nucleoplasm part Any constituent part of the nucleoplasm, that part of the nuclear content other than the chromosomes or the nucleolus. cell part Any constituent part of a cell, the basic structural and functional unit of all organisms. NIF_Subcellular:sao628508602 cellular subcomponent single-organism process A biological process that involves only one organism. single organism process single-organism metabolic process A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism. mature miRNA 3'-end processing Any process involved in forming distinct miRNA isoforms from a mature miRNA that differ at their 3'-ends. 3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule that contributes to forming distinct miRNA isoforms from a mature miRNA. single-organism cellular process Any process that is carried out at the cellular level, occurring within a single organism. single-organism transport The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving a single organism. negative regulation of transcription, DNA-templated Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. down regulation of transcription, DNA-dependent down-regulation of transcription, DNA-dependent downregulation of transcription, DNA-dependent negative regulation of cellular transcription, DNA-dependent negative regulation of transcription, DNA-dependent positive regulation of transcription, DNA-templated Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. positive regulation of cellular transcription, DNA-dependent positive regulation of transcription, DNA-dependent up regulation of transcription, DNA-dependent up-regulation of transcription, DNA-dependent upregulation of transcription, DNA-dependent negative regulation of nucleobase-containing compound metabolic process Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism positive regulation of nucleobase-containing compound metabolic process Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process positive regulation of transcription from RNA polymerase II promoter Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter. activation of transcription from RNA polymerase II promoter positive regulation of transcription from Pol II promoter stimulation of transcription from RNA polymerase II promoter up regulation of transcription from RNA polymerase II promoter up-regulation of transcription from RNA polymerase II promoter upregulation of transcription from RNA polymerase II promoter heterocycle metabolic process The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle metabolism heterocycle catabolic process The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle breakdown heterocycle catabolism heterocycle degradation intracellular transport The directed movement of substances within a cell. positive regulation of biological process Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. positive regulation of physiological process up regulation of biological process up-regulation of biological process upregulation of biological process negative regulation of biological process Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. down regulation of biological process down-regulation of biological process downregulation of biological process negative regulation of physiological process positive regulation of cellular process Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. positive regulation of cellular physiological process up regulation of cellular process up-regulation of cellular process upregulation of cellular process negative regulation of cellular process Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. down regulation of cellular process down-regulation of cellular process downregulation of cellular process negative regulation of cellular physiological process regulation of response to stimulus Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. positive regulation of response to stimulus Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. up regulation of response to stimulus up-regulation of response to stimulus upregulation of response to stimulus negative regulation of response to stimulus Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. down regulation of response to stimulus down-regulation of response to stimulus downregulation of response to stimulus RNA transport The directed movement of RNA, ribonucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. regulation of biological process Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. regulation of physiological process regulation of cellular process Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. regulation of cellular physiological process response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. physiological response to stimulus nuclear export Reactome:REACT_10069 Reactome:REACT_103510 Reactome:REACT_112801 Reactome:REACT_113944 Reactome:REACT_31254 Reactome:REACT_83378 Reactome:REACT_89070 Reactome:REACT_92337 Reactome:REACT_92521 Reactome:REACT_92868 Reactome:REACT_96465 The directed movement of substances out of the nucleus. export from nucleus nucleus export substance nuclear export regulation of nitrogen compound metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. regulation of nitrogen metabolic process regulation of nitrogen metabolism negative regulation of nitrogen compound metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. down regulation of nitrogen metabolic process down-regulation of nitrogen metabolic process downregulation of nitrogen metabolic process negative regulation of nitrogen metabolic process negative regulation of nitrogen metabolism positive regulation of nitrogen compound metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. positive regulation of nitrogen metabolic process positive regulation of nitrogen metabolism up regulation of nitrogen metabolic process up-regulation of nitrogen metabolic process upregulation of nitrogen metabolic process localization Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to or maintained in a specific location. establishment and maintenance of localization establishment and maintenance of position localisation establishment of localization The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location. establishment of localisation establishment of RNA localization RNA positioning RNA recruitment The directed movement of RNA to a specific location. establishment of RNA localisation regulation of protein metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein. regulation of protein metabolism negative regulation of protein metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein. down regulation of protein metabolic process down-regulation of protein metabolic process downregulation of protein metabolic process negative regulation of protein metabolism regulation of RNA metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA. regulation of RNA metabolism negative regulation of RNA metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA. down regulation of RNA metabolic process down-regulation of RNA metabolic process downregulation of RNA metabolic process negative regulation of RNA metabolism positive regulation of RNA metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA. positive regulation of RNA metabolism up regulation of RNA metabolic process up-regulation of RNA metabolic process upregulation of RNA metabolic process cellular response to stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. regulation of posttranscriptional gene silencing Any process that modulates the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism. positive regulation of posttranscriptional gene silencing Any process that increases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism. negative regulation of posttranscriptional gene silencing Any process that decreases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism. regulation of macromolecule metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. regulation of gene silencing by miRNA Any process that modulates the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression. regulation of gene silencing by microRNA negative regulation of gene silencing by miRNA Any process that decreases the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression. negative regulation of gene silencing by microRNA regulation of gene silencing by RNA Any process that regulates the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes. negative regulation of gene silencing by RNA Any process that decreases the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes. regulation of gene silencing Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation. negative regulation of gene silencing Any process that decreases the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation. pri-miRNA transcription from RNA polymerase II promoter The cellular synthesis of primary microRNA (pri-miRNA) transcripts from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. pri-miRNA transcripts are subsequently processed to produce the ~22nt miRNAs that function in gene regulation. macromolecular complex assembly The aggregation, arrangement and bonding together of a set of macromolecules to form a complex. macromolecule complex assembly intracellular organelle lumen An organelle lumen that is part of an intracellular organelle. RISC-loading complex A trimeric ribonucleoprotein complex that and is required for the formation of a mature RNA induced silencing complex (RISC). In humans the complex is composed of the endonuclease Dicer (DICER1) and TRBP (TARBP2) in association with the Argonaute protein Ago2 (EIF2C2/AGO2). Within the complex, Dicer and TRBP are required to process precursor miRNAs (pre-miRNAs) to mature miRNAs and then load them onto Ago2. Ago2 bound to the mature miRNA constitutes the minimal RISC and may subsequently dissociate from Dicer and TRBP. This complex has endorobonuclease activity. miRLC microRNA loading complex microprocessor complex A protein complex that binds to heme and to pri-miRNAs, and is required for the formation of a pre-microRNA (pre-miRNA), the initial step of microRNA (miRNA) biogenesis. The complex is composed of the double-stranded-RNA-specific RNase Drosha (also called RNASEN) and the RNA-binding protein DGCR8 (heme-free or heme-bound forms). Within the complex, DGCR8 function as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs RNASEN/Drosha to cleave the 3' and 5' strands of a stem-loop to release hairpin-shaped pre-miRNAs. IntAct:EBI-9519039 IntAct:EBI-9519056 primary miRNA binding Interacting selectively and non-covalently with a primary microRNA (pri-miRNA) transcript, an RNA molecule that is processed into a short hairpin-shaped structure called a pre-miRNA and finally into a functional miRNA. Both double-stranded and single-stranded regions of a pri-miRNA are required for binding. pri-miRNA binding primary microRNA binding pre-miRNA binding Interacting selectively and non-covalently with a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA. pre-microRNA binding precursor microRNA binding cellular response to chemical stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. production of small RNA involved in gene silencing by RNA The process in which a double-stranded RNA precursor is processed into short (20-30 nt) fragments. RNA cleavage is catalyzed by a Dicer endonuclease. gene silencing by RNA, production of guide RNA gene silencing by RNA, production of small RNA regulation of production of small RNA involved in gene silencing by RNA Any process that modulates the frequency, rate or extent of the production of small RNA involved in gene silencing by RNA. regulation of gene silencing by RNA, production of guide RNA regulation of gene silencing by RNA, production of small RNA ribonucleoprotein complex localization Any process in which a ribonucleoprotein complex is transported to, or maintained in, a specific location within a cell. RNP localization cellular ribonucleoprotein complex localization establishment and maintenance of ribonucleoprotein complex localization ribonucleoprotein complex localisation cellular response to organic substance Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus. cellular response to dsRNA Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a double-stranded RNA stimulus. cellular response to double-stranded RNA cellular response to organic cyclic compound Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus. cellular response to organic cyclic substance ribonucleoprotein complex export from nucleus RNP export from nucleus The directed movement of a ribonucleoprotein complex from the nucleus to the cytoplasm. ribonucleoprotein complex export from cell nucleus ribonucleoprotein complex nucleus export ribonucleoprotein complex transport from nucleus to cytoplasm pre-miRNA-containing ribonucleoprotein complex export from nucleus The directed movement of a ribonucleoprotein complex that contains pre-microRNA from the nucleus to the cytoplasm. pre-microRNA-containing RNP export from nucleus pre-microRNA-containing ribonucleoprotein complex export from cell nucleus pre-microRNA-containing ribonucleoprotein complex export from nucleus pre-microRNA-containing ribonucleoprotein complex nucleus export pre-microRNA-containing ribonucleoprotein complex transport from nucleus to cytoplasm organic substance metabolic process The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. organic molecular entity metabolic process organic molecular entity metabolism organic substance metabolism cellular component organization or biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level regulation of primary metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. nucleic acid metabolic process Any cellular metabolic process involving nucleic acids. nucleic acid phosphodiester bond hydrolysis The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis. nucleic acid cleavage RNA phosphodiester bond hydrolysis The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis. RNA phosphodiester bond hydrolysis, endonucleolytic The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides. RNA phosphodiester bond hydrolysis, exonucleolytic The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides. endoribonuclease activity, cleaving miRNA-paired mRNA Catalysis of the endonucleolytic cleavage of the mRNA in a double-stranded RNA molecule formed by the base pairing of an mRNA with an miRNA. pre-miRNA transporter activity Enables the directed movement of pre-miRNAs between the nucleus and the cytoplasm of a cell. organic cyclic compound metabolic process The chemical reactions and pathways involving organic cyclic compound. organic cyclic compound metabolism organic cyclic compound catabolic process The chemical reactions and pathways resulting in the breakdown of organic cyclic compound. organic cyclic compound breakdown organic cyclic compound catabolism organic cyclic compound degradation organic cyclic compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic cyclic compound. organic cyclic compound anabolism organic cyclic compound biosynthesis organic cyclic compound formation organic cyclic compound synthesis organic substance catabolic process The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon. organic molecular entity breakdown organic molecular entity catabolic process organic molecular entity catabolism organic molecular entity degradation organic substance breakdown organic substance catabolism organic substance degradation organic substance biosynthetic process The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. organic molecular entity anabolism organic molecular entity biosynthesis organic molecular entity biosynthetic process organic molecular entity formation organic molecular entity synthesis organic substance anabolism organic substance biosynthesis organic substance formation organic substance synthesis response to nitrogen compound Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus. response to nitrogen molecular entity cellular response to nitrogen compound Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus. cellular response to nitrogen molecular entity negative regulation of RNA catabolic process Any process that stops, prevents or reduces the frequency, rate or extent of RNA catabolic process. down regulation of RNA breakdown down regulation of RNA catabolic process down regulation of RNA catabolism down regulation of RNA degradation down-regulation of RNA breakdown down-regulation of RNA catabolic process down-regulation of RNA catabolism down-regulation of RNA degradation downregulation of RNA breakdown downregulation of RNA catabolic process downregulation of RNA catabolism downregulation of RNA degradation negative regulation of RNA breakdown negative regulation of RNA catabolism negative regulation of RNA degradation single-organism localization A localization which involves only one organism. single organism localization single-organism intracellular transport An intracellular transport which involves only one organism. single organism intracellular transport negative regulation of RNA biosynthetic process Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process. down regulation of RNA anabolism down regulation of RNA biosynthesis down regulation of RNA biosynthetic process down regulation of RNA formation down regulation of RNA synthesis down-regulation of RNA anabolism down-regulation of RNA biosynthesis down-regulation of RNA biosynthetic process down-regulation of RNA formation down-regulation of RNA synthesis downregulation of RNA anabolism downregulation of RNA biosynthesis downregulation of RNA biosynthetic process downregulation of RNA formation downregulation of RNA synthesis negative regulation of RNA anabolism negative regulation of RNA biosynthesis negative regulation of RNA formation negative regulation of RNA synthesis positive regulation of RNA biosynthetic process Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process. positive regulation of RNA anabolism positive regulation of RNA biosynthesis positive regulation of RNA formation positive regulation of RNA synthesis up regulation of RNA anabolism up regulation of RNA biosynthesis up regulation of RNA biosynthetic process up regulation of RNA formation up regulation of RNA synthesis up-regulation of RNA anabolism up-regulation of RNA biosynthesis up-regulation of RNA biosynthetic process up-regulation of RNA formation up-regulation of RNA synthesis upregulation of RNA anabolism upregulation of RNA biosynthesis upregulation of RNA biosynthetic process upregulation of RNA formation upregulation of RNA synthesis regulation of pri-miRNA transcription from RNA polymerase II promoter Any process that modulates the frequency, rate or extent of pri-miRNA transcription from RNA polymerase II promoter. negative regulation of pri-miRNA transcription from RNA polymerase II promoter Any process that stops, prevents or reduces the frequency, rate or extent of pri-miRNA transcription from RNA polymerase II promoter. down regulation of pri-miRNA transcription from RNA polymerase II promoter down-regulation of pri-miRNA transcription from RNA polymerase II promoter downregulation of pri-miRNA transcription from RNA polymerase II promoter positive regulation of pri-miRNA transcription from RNA polymerase II promoter Any process that activates or increases the frequency, rate or extent of pri-miRNA transcription from RNA polymerase II promoter. up regulation of pri-miRNA transcription from RNA polymerase II promoter up-regulation of pri-miRNA transcription from RNA polymerase II promoter upregulation of pri-miRNA transcription from RNA polymerase II promoter regulation of nucleic acid-templated transcription Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription. negative regulation of nucleic acid-templated transcription Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription. down regulation of nucleic acid-templated transcription down-regulation of nucleic acid-templated transcription downregulation of nucleic acid-templated transcription positive regulation of nucleic acid-templated transcription Any process that activates or increases the frequency, rate or extent of nucleic acid-templated transcription. up regulation of nucleic acid-templated transcription up-regulation of nucleic acid-templated transcription upregulation of nucleic acid-templated transcription regulation of production of miRNAs involved in gene silencing by miRNA Any process that modulates the frequency, rate or extent of production of miRNAs involved in gene silencing by miRNA. regulation of gene silencing by miRNA, production of miRNAs regulation of miRNA processing regulation of miRNA-mediated gene silencing, production of miRNAs regulation of microRNA-mediated gene silencing, production of microRNAs regulation of production of microRNAs involved in gene silencing by microRNA negative regulation of production of miRNAs involved in gene silencing by miRNA Any process that stops, prevents or reduces the frequency, rate or extent of production of miRNAs involved in gene silencing by miRNA. down regulation of gene silencing by miRNA, production of miRNAs down regulation of miRNA processing down regulation of miRNA-mediated gene silencing, production of miRNAs down regulation of microRNA-mediated gene silencing, production of microRNAs down regulation of production of miRNAs involved in gene silencing by miRNA down regulation of production of microRNAs involved in gene silencing by microRNA down-regulation of gene silencing by miRNA, production of miRNAs down-regulation of miRNA processing down-regulation of miRNA-mediated gene silencing, production of miRNAs down-regulation of microRNA-mediated gene silencing, production of microRNAs down-regulation of production of miRNAs involved in gene silencing by miRNA down-regulation of production of microRNAs involved in gene silencing by microRNA downregulation of gene silencing by miRNA, production of miRNAs downregulation of miRNA processing downregulation of miRNA-mediated gene silencing, production of miRNAs downregulation of microRNA-mediated gene silencing, production of microRNAs downregulation of production of miRNAs involved in gene silencing by miRNA downregulation of production of microRNAs involved in gene silencing by microRNA negative regulation of gene silencing by miRNA, production of miRNAs negative regulation of miRNA processing negative regulation of miRNA-mediated gene silencing, production of miRNAs negative regulation of microRNA-mediated gene silencing, production of microRNAs negative regulation of production of microRNAs involved in gene silencing by microRNA positive regulation of production of miRNAs involved in gene silencing by miRNA Any process that activates or increases the frequency, rate or extent of production of miRNAs involved in gene silencing by miRNA. positive regulation of gene silencing by miRNA, production of miRNAs positive regulation of miRNA processing positive regulation of miRNA-mediated gene silencing, production of miRNAs positive regulation of microRNA-mediated gene silencing, production of microRNAs positive regulation of production of microRNAs involved in gene silencing by microRNA up regulation of gene silencing by miRNA, production of miRNAs up regulation of miRNA processing up regulation of miRNA-mediated gene silencing, production of miRNAs up regulation of microRNA-mediated gene silencing, production of microRNAs up regulation of production of miRNAs involved in gene silencing by miRNA up regulation of production of microRNAs involved in gene silencing by microRNA up-regulation of gene silencing by miRNA, production of miRNAs up-regulation of miRNA processing up-regulation of miRNA-mediated gene silencing, production of miRNAs up-regulation of microRNA-mediated gene silencing, production of microRNAs up-regulation of production of miRNAs involved in gene silencing by miRNA up-regulation of production of microRNAs involved in gene silencing by microRNA upregulation of gene silencing by miRNA, production of miRNAs upregulation of miRNA processing upregulation of miRNA-mediated gene silencing, production of miRNAs upregulation of microRNA-mediated gene silencing, production of microRNAs upregulation of production of miRNAs involved in gene silencing by miRNA upregulation of production of microRNAs involved in gene silencing by microRNA miRNA transport The directed movement of microRNA (miRNA) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. microRNA transport protein-lipid-RNA complex A macromolecular complex containing separate protein, lipid and RNA molecules. Separate in this context means not covalently bound to each other. HDL-containing protein-lipid-RNA complex A protein-lipid-RNA complex containing separate high-density lipoprotein (HDL), lipid and RNA molecules. Separate in this context means not covalently bound to each other. LDL-containing protein-lipid-RNA complex A protein-lipid-RNA complex containing separate low-density lipoprotein (LDL), lipid and RNA molecules. Separate in this context means not covalently bound to each other. primary miRNA modification The covalent alteration of one or more nucleotides within a primary miRNA molecule to produce a primary miRNA molecule with a sequence that differs from that coded genetically. regulation of cellular macromolecule biosynthetic process Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process. regulation of cellular biopolymer biosynthetic process regulation of cellular macromolecule anabolism regulation of cellular macromolecule biosynthesis regulation of cellular macromolecule formation regulation of cellular macromolecule synthesis negative regulation of cellular macromolecule biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process. negative regulation of cellular biopolymer biosynthetic process negative regulation of cellular macromolecule anabolism negative regulation of cellular macromolecule biosynthesis negative regulation of cellular macromolecule formation negative regulation of cellular macromolecule synthesis regulation of miRNA catabolic process Any process that modulates the frequency, rate or extent of miRNA catabolic process. regulation of microRNA catabolic process negative regulation of miRNA catabolic process Any process that stops, prevents or reduces the frequency, rate or extent of miRNA catabolic process. negative regulation of microRNA catabolic process positive regulation of miRNA catabolic process Any process that activates or increases the frequency, rate or extent of miRNA catabolic process. positive regulation of microRNA catabolic process regulation of miRNA metabolic process Any process that modulates the frequency, rate or extent of miRNA metabolic process. regulation of microRNA metabolic process negative regulation of miRNA metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of miRNA metabolic process. negative regulation of microRNA metabolic process positive regulation of miRNA metabolic process Any process that activates or increases the frequency, rate or extent of miRNA metabolic process. positive regulation of microRNA metabolic process regulation of pre-miRNA processing Any process that modulates the frequency, rate or extent of pre-microRNA processing. regulation of pre-microRNA processing negative regulation of pre-miRNA processing Any process that stops, prevents or reduces the frequency, rate or extent of pre-microRNA processing. negative regulation of pre-microRNA processing positive regulation of pre-miRNA processing Any process that activates or increases the frequency, rate or extent of pre-microRNA processing. positive regulation of pre-microRNA processing regulation of primary miRNA processing Any process that modulates the frequency, rate or extent of primary microRNA processing. regulation of pri-miRNA processing regulation of primary microRNA processing negative regulation of primary miRNA processing Any process that stops, prevents or reduces the frequency, rate or extent of primary microRNA processing. negative regulation of pri-miRNA processing negative regulation of primary microRNA processing positive regulation of primary miRNA processing Any process that activates or increases the frequency, rate or extent of primary microRNA processing. positive regulation of pri-miRNA processing positive regulation of primary microRNA processing positive regulation of gene silencing by miRNA Any process that activates or increases the frequency, rate or extent of gene silencing by miRNA. positive regulation of miRNA-mediated gene silencing positive regulation of microRNA-mediated gene silencing regulation of RNA biosynthetic process Any process that modulates the frequency, rate or extent of RNA biosynthetic process. regulation of RNA anabolism regulation of RNA biosynthesis regulation of RNA formation regulation of RNA synthesis 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 curation status specification Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 PERSON:Bill Bug The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. curation status specification data about an ontology part Person:Alan Ruttenberg data about an ontology part is a data item about a part of an ontology, for example a term obsolescence reason specification PERSON: Alan Ruttenberg PERSON: Melanie Courtot The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. obsolescence reason specification denotator type A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. miRNA_target_gene_primary_transcript miRNA_target_gene_mRNA miRNA_and_target_gene_binding fly_miRNA c_elegans_miRNA bacterial_miRNA virus_miRNA non_mammalian_miRNA mammalian_miRNA miRNA_expression protein_miRNA_promoter_binding promoter_of_miRNA miRNA_transcription_initiation transcription_of_miRNA animal_study_model miRNA_target_gene 2015-05-25T15:37:18Z environmental_variable 2013-09-28T19:15:26Z An experimental variable is the variable that is used in an experiment and is known as the dependent variable that can be manipulated and is being studied HeZhang gene_sequence 2013-09-28T19:15:26Z HeZhang pressure 2013-09-28T19:16:26Z HeZhang The ratio of force to the area over which that force is distributed temperature 2013-09-28T19:16:26Z HeZhang Numerical measure of hot or cold high_pressure 2013-09-28T19:17:41Z HeZhang low_pressure 2013-09-28T19:17:41Z HeZhang normal_pressure 2013-09-28T19:17:41Z HeZhang high_temperature 2013-09-28T19:18:33Z HeZhang low_temperature 2013-09-28T19:18:33Z HeZhang normal_temperature 2013-09-28T19:18:33Z HeZhang harmful_role "A harmful role or activity realizeable by some agent in the human body" 2013-09-29T18:27:09Z HeZhang harmful_environmental_effect "Harmful physical agents" 2013-09-29T18:29:20Z HeZhang pathogenicity ""Germs" -- foreign microorganisms capable of causing disease" 2013-09-29T18:29:20Z HeZhang The potential capacity of certain species of microbes to cause a disease toxic_activity "Harmful chemical agents" 2013-09-29T18:29:20Z HeZhang carcinogenicity The ability or tendency to produce cancer. 2013-09-29T18:30:22Z HeZhang virus 2013-10-01T23:27:46Z HeZhang Small infectious agent that replicates only inside the living cells of other organisms adult_tissue 2013-10-01T23:32:05Z HeZhang embryonic_tissue "Tissues existing in the early embryonic stages of development" 2013-10-01T23:32:05Z HeZhang Tissue in an embryo connective_tissue "Tissues originating from mesoderm and performing a structural or connective function between other tissues" 2013-10-01T23:33:33Z HeZhang Tissue that connects, supports, binds, or separates other tissues or organs, typically having relatively few cells embedded in an amorphous matrix, often with collagen or other fibers, and including cartilaginous, fatty, and elastic tissues. epithelia_tissue "Tissue lining body structures and forming glands" 2013-10-01T23:33:33Z HeZhang Membranous tissue covering internal organs and other internal surfaces of the body. muscle_tissue "Tissue forming muscles - capable of generating movement of body structures" 2013-10-01T23:33:33Z HeZhang Muscle tissue is one of four basic biological tissues present in animals. It is a soft tissue that composes muscles. It is formed during embryo development in a process known as myogenesis. nerve_tissue "Tissue forming nerves and neural structures like the brain and spinal cord, used for coordinating bodily functions." 2013-10-01T23:33:33Z HeZhang Tissue composed of neurons. adipose_tissue "Fat tissue" 2013-10-01T23:34:55Z A kind of body tissue containing stored fat that serves as a source of energy; it also cushions and insulates vital organs. HeZhang blood "Blood tissue, including red and white blood cells" 2013-10-01T23:34:55Z Bodily fluid in animals that delivers necessary substances such as nutrients and oxygen to the cells and transports metabolic waste products away. HeZhang bone "Bone tissue - provides structural framework for body with high compressive strength" 2013-10-01T23:34:55Z HeZhang Rigid organs that constitute part of the endoskeleton of vertebrates. cartilage "Tough tissue that connects bones and gives form to many of the soft structures of the body" 2013-10-01T23:34:55Z A tough, elastic, fibrous connective tissue found in various parts of the body, such as the joints, outer ear, and larynx. HeZhang cardiac_muscle "Muscle cells of the heart" 2013-10-01T23:36:04Z HeZhang Type of involuntary striated muscle found in the walls and histological foundation of the heart. skeletal_muscle "Muscle cells of skeletal muscle - those that execute voluntary movement of the skeleton" 2013-10-01T23:36:04Z Form of striated muscle tissue which is under the control of the somatic nervous system. HeZhang smooth_muscle "Muscle cells of smooth muscle - found in digestive tract and blood vessels, execute involuntary movement" 2013-10-01T23:36:04Z HeZhang Responsible for the contractility of hollow organs, such as blood vessels, the gastrointestinal tract, the bladder, or the uterus. ectoderm "The outer layer of cells in the early embryo" 2013-10-03T23:21:30Z HeZhang Outermost of the three primary germ layers of an embryo, from which the epidermis, nervous tissue, and, in vertebrates, sense organs develop. endoderm "The inner layer of cells in the early embryo" 2013-10-03T23:21:30Z HeZhang Innermost of the three primary germ layers of an animal embryo, developing into the gastrointestinal tract, the lungs, and associated structures. mesoderm "The middle layer of cells in the early embryo" 2013-10-03T23:21:30Z HeZhang Middle embryonic germ layer, lying between the ectoderm and the endoderm, from which connective tissue, muscle, bone, and the urogenital and circulatory systems develop. treatment 2013-10-03T23:37:16Z HeZhang pharmaceutical_treatment 2013-10-04T20:10:02Z physical_therapy 2013-10-04T20:10:02Z A health care profession primarily concerned with the remediation of impairments and disabilities and the promotion of mobility, functional ability, quality of life and movement potential through examination, evaluation, diagnosis and physical intervention. psychological_treatment 2013-10-04T20:10:02Z surgery 2013-10-04T20:10:02Z Branch of medicine that deals with the diagnosis and treatment of injury, deformity, and disease by manual and instrumental means. analgesic_treatment 2013-10-04T20:19:18Z antibiotic_treatment 2013-10-04T20:19:18Z antihyperlipidemic_treatment 2013-10-04T20:19:18Z antihypertensive_treatment 2013-10-04T20:19:18Z chemotherapy 2013-10-04T20:19:18Z Treatment of cancer with one or more cytotoxic antineoplastic drugs. immunosuppressive_therapy 2013-10-04T20:19:18Z Immunosuppression involves an act that reduces the activation or efficacy of the immune system. radiation_release 2013-10-04T20:24:14Z The treatment of disease, esp. cancer, using X-rays or similar forms of radiation. cellular_organism 2013-10-07T00:19:58Z An organism of microscopic or submicroscopic size, especially a bacterium or protozoan archaea 2013-10-07T00:31:14Z HeZhang microorganisms that are similar to bacteria in size and simplicity of structure but radically different in molecular organization. They are now believed to constitute an ancient intermediate group between the bacteria and eukaryotes bacteria 2013-10-07T00:31:14Z HeZhang a member of a large group of unicellular microorganisms that have cell walls but lack organelles and an organized nucleus, including some that can cause diseas mouse_miRNA TE_juxtaposition 2013-10-25T16:05:06Z HeZhang TE_insertion 2013-10-25T16:03:19Z positive_strand_insertion 2013-10-25T16:17:26Z HeZhang negative_strand_insertion 2013-10-25T16:17:26Z HeZhang human_miRNA 2015-05-16T19:26:04Z He_Zhang hsa-mir-585 miRBase:MI0003592 hsa-mir-620 miRBase:MI0003634 hsa-mir-659 miRBase:MI0003683 hsa-mir-2113 miRBase:MI0003939 hsa-mir-1229 miRBase:MI0006319 hsa-mir-1234 miRBase:MI0006324 hsa-mir-548o miRBase:MI0006402 hsa-mir-1279 miRBase:MI0006426 hsa-mir-1321 miRBase:MI0006652 hsa-mir-1470 miRBase:MI0007075 hsa-mir-1539 miRBase:MI0007260 hsa-mir-1973 miRBase:MI0009983 hsa-mir-2052 miRBase:MI0010486 hsa-mir-2053 miRBase:MI0010487 hsa-mir-2054 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mir-627 miRBase:MIPF0000550 mir-554 miRBase:MIPF0000551 mir-767 miRBase:MIPF0000552 mir-618 miRBase:MIPF0000553 mir-887 miRBase:MIPF0000554 mir-567 miRBase:MIPF0000555 mir-644 miRBase:MIPF0000556 mir-619 miRBase:MIPF0000557 mir-1307 miRBase:MIPF0000558 mir-1285 miRBase:MIPF0000559 mir-937 miRBase:MIPF0000560 mir-573 miRBase:MIPF0000561 mir-604 miRBase:MIPF0000562 mir-587 miRBase:MIPF0000563 mir-1244 miRBase:MIPF0000569 mir-566 miRBase:MIPF0000576 mir-1233 miRBase:MIPF0000578 mir-1273 miRBase:MIPF0000579 mir-555 miRBase:MIPF0000583 mir-1297 miRBase:MIPF0000584 mir-1237 miRBase:MIPF0000585 mir-575 miRBase:MIPF0000586 mir-1282 miRBase:MIPF0000587 mir-1324 miRBase:MIPF0000589 mir-613 miRBase:MIPF0000590 mir-1278 miRBase:MIPF0000591 mir-1184 miRBase:MIPF0000592 mir-1256 miRBase:MIPF0000594 mir-1262 miRBase:MIPF0000595 mir-1207 miRBase:MIPF0000596 mir-637 miRBase:MIPF0000597 mir-1298 miRBase:MIPF0000598 mir-1291 miRBase:MIPF0000599 mir-634 miRBase:MIPF0000600 mir-1178 miRBase:MIPF0000601 mir-1294 miRBase:MIPF0000603 mir-1284 miRBase:MIPF0000604 mir-646 miRBase:MIPF0000605 mir-935 miRBase:MIPF0000606 mir-1303 miRBase:MIPF0000608 mir-1205 miRBase:MIPF0000609 mir-1290 miRBase:MIPF0000610 mir-1253 miRBase:MIPF0000611 mir-564 miRBase:MIPF0000612 mir-1202 miRBase:MIPF0000613 mir-1254 miRBase:MIPF0000614 mir-1266 miRBase:MIPF0000615 mir-1323 miRBase:MIPF0000617 mir-622 miRBase:MIPF0000619 mir-1245 miRBase:MIPF0000620 mir-1251 miRBase:MIPF0000621 mir-1248 miRBase:MIPF0000622 mir-561 miRBase:MIPF0000623 mir-762 miRBase:MIPF0000624 mir-1299 miRBase:MIPF0000625 mir-1289 miRBase:MIPF0000626 mir-1246 miRBase:MIPF0000627 mir-1208 miRBase:MIPF0000628 mir-621 miRBase:MIPF0000631 mir-1179 miRBase:MIPF0000632 mir-1203 miRBase:MIPF0000633 mir-1206 miRBase:MIPF0000634 mir-1267 miRBase:MIPF0000640 mir-591 miRBase:MIPF0000641 mir-658 miRBase:MIPF0000643 mir-1272 miRBase:MIPF0000645 mir-1827 miRBase:MIPF0000646 mir-614 miRBase:MIPF0000647 mir-1296 miRBase:MIPF0000649 mir-595 miRBase:MIPF0000651 mir-1276 miRBase:MIPF0000652 mir-630 miRBase:MIPF0000653 mir-559 miRBase:MIPF0000656 mir-645 miRBase:MIPF0000657 mir-302_2 miRBase:MIPF0000658 mir-1288 miRBase:MIPF0000660 mir-610 miRBase:MIPF0000661 mir-635 miRBase:MIPF0000662 mir-1322 miRBase:MIPF0000663 mir-1181 miRBase:MIPF0000665 mir-1249 miRBase:MIPF0000667 mir-1183 miRBase:MIPF0000668 mir-1247 miRBase:MIPF0000669 mir-1825 miRBase:MIPF0000670 mir-1204 miRBase:MIPF0000671 mir-617 miRBase:MIPF0000672 mir-1182 miRBase:MIPF0000673 mir-1275 miRBase:MIPF0000674 mir-1292 miRBase:MIPF0000675 mir-1295 miRBase:MIPF0000676 mir-766 miRBase:MIPF0000677 mir-641 miRBase:MIPF0000679 mir-588 miRBase:MIPF0000681 mir-1286 miRBase:MIPF0000682 mir-1258 miRBase:MIPF0000684 mir-1263 miRBase:MIPF0000687 mir-1265 miRBase:MIPF0000688 mir-1236 miRBase:MIPF0000689 mir-943 miRBase:MIPF0000690 mir-1293 miRBase:MIPF0000691 mir-1281 miRBase:MIPF0000695 mir-1250 miRBase:MIPF0000696 mir-759 miRBase:MIPF0000706 mir-764 miRBase:MIPF0000707 mir-761 miRBase:MIPF0000709 mir-1193 miRBase:MIPF0000714 mir-718 miRBase:MIPF0000721 mir-1287 miRBase:MIPF0000725 mir-769 miRBase:MIPF0000727 mir-670 miRBase:MIPF0000734 mir-1301 miRBase:MIPF0000742 mir-711 miRBase:MIPF0000748 mir-571 miRBase:MIPF0000757 mir-602 miRBase:MIPF0000767 mir-1912 miRBase:MIPF0000768 mir-1468 miRBase:MIPF0000777 mir-606 miRBase:MIPF0000780 mir-1180 miRBase:MIPF0000789 mir-623 miRBase:MIPF0000798 mir-1261 miRBase:MIPF0000802 mir-596 miRBase:MIPF0000808 mir-3130 miRBase:MIPF0000845 mir-3202 miRBase:MIPF0000846 mir-1270 miRBase:MIPF0000877 mir-3156 miRBase:MIPF0000891 mir-3180 miRBase:MIPF0000894 mir-3179 miRBase:MIPF0000900 mir-1538 miRBase:MIPF0000903 mir-1537 miRBase:MIPF0000917 mir-4283 miRBase:MIPF0000919 mir-1228 miRBase:MIPF0000924 mir-2355 miRBase:MIPF0000938 mir-647 miRBase:MIPF0000939 mir-1238 miRBase:MIPF0000941 mir-1268 miRBase:MIPF0000946 mir-2861 miRBase:MIPF0000963 mir-1305 miRBase:MIPF0000965 mir-1252 miRBase:MIPF0000968 mir-3119 miRBase:MIPF0000971 mir-608 miRBase:MIPF0000972 mir-1909 miRBase:MIPF0000973 mir-1469 miRBase:MIPF0000979 mir-921 miRBase:MIPF0000982 mir-1269 miRBase:MIPF0000984 mir-1910 miRBase:MIPF0000987 mir-1257 miRBase:MIPF0000998 mir-3116 miRBase:MIPF0001002 mir-1913 miRBase:MIPF0001015 mir-1260a miRBase:MIPF0001020 mir-1908 miRBase:MIPF0001021 mir-1972 miRBase:MIPF0001025 mir-3199 miRBase:MIPF0001026 mir-3160 miRBase:MIPF0001028 mir-4315 miRBase:MIPF0001033 mir-1200 miRBase:MIPF0001036 mir-1915 miRBase:MIPF0001037 mir-1914 miRBase:MIPF0001040 mir-1304 miRBase:MIPF0001064 mir-3158 miRBase:MIPF0001065 mir-1471 miRBase:MIPF0001069 mir-3150 miRBase:MIPF0001102 mir-3074 miRBase:MIPF0001103 mir-3065 miRBase:MIPF0001105 mir-3926 miRBase:MIPF0001118 mir-3913 miRBase:MIPF0001134 mir-3689 miRBase:MIPF0001144 mir-3910 miRBase:MIPF0001148 mir-3914 miRBase:MIPF0001169 mir-3622 miRBase:MIPF0001179 mir-1343 miRBase:MIPF0001206 mir-4509 miRBase:MIPF0001207 mir-4776 miRBase:MIPF0001210 mir-3198 miRBase:MIPF0001216 mir-3135 miRBase:MIPF0001219 mir-4435 miRBase:MIPF0001220 mir-4679 miRBase:MIPF0001228 mir-4650 miRBase:MIPF0001234 mir-4436 miRBase:MIPF0001236 mir-3064 miRBase:MIPF0001238 mir-3155 miRBase:MIPF0001242 mir-4662 miRBase:MIPF0001245 mir-4773 miRBase:MIPF0001250 mir-3190 miRBase:MIPF0001251 mir-4659 miRBase:MIPF0001256 mir-4771 miRBase:MIPF0001258 mir-3529 miRBase:MIPF0001261 mir-3688 miRBase:MIPF0001263 mir-3960 miRBase:MIPF0001271 mir-4520 miRBase:MIPF0001272 mir-4477 miRBase:MIPF0001274 mir-1231 miRBase:MIPF0001309 mir-4444 miRBase:MIPF0001310 mir-4536 miRBase:MIPF0001319 mir-5701 miRBase:MIPF0001325 mir-4524 miRBase:MIPF0001330 mir-3680 miRBase:MIPF0001338 mir-3670 miRBase:MIPF0001340 mir-5681 miRBase:MIPF0001343 mir-5692 miRBase:MIPF0001351 mir-5583 miRBase:MIPF0001356 mir-1260b miRBase:MIPF0001381 mir-6511 miRBase:MIPF0001382 mir-3173 miRBase:MIPF0001383 mir-4743 miRBase:MIPF0001384 mir-4446 miRBase:MIPF0001385 mir-3154 miRBase:MIPF0001387 mir-4667 miRBase:MIPF0001390 mir-3151 miRBase:MIPF0001394 mir-3660 miRBase:MIPF0001397 mir-2110 miRBase:MIPF0001399 mir-3943 miRBase:MIPF0001400 mir-3193 miRBase:MIPF0001401 mir-4796 miRBase:MIPF0001402 mir-6127 miRBase:MIPF0001405 mir-3613 miRBase:MIPF0001411 mir-6131 miRBase:MIPF0001412 mir-6130 miRBase:MIPF0001413 mir-6133 miRBase:MIPF0001415 mir-3121 miRBase:MIPF0001417 mir-6129 miRBase:MIPF0001423 mir-3145 miRBase:MIPF0001427 mir-3138 miRBase:MIPF0001428 mir-23c miRBase:MIPF0001429 mir-6132 miRBase:MIPF0001438 mir-3127 miRBase:MIPF0001439 mir-4484 miRBase:MIPF0001440 mir-3200 miRBase:MIPF0001441 mir-6128 miRBase:MIPF0001442 mir-6134 miRBase:MIPF0001445 mir-4529 miRBase:MIPF0001451 mir-3129 miRBase:MIPF0001458 mir-4660 miRBase:MIPF0001460 mir-3927 miRBase:MIPF0001462 mir-378_2 miRBase:MIPF0001463 mir-2114 miRBase:MIPF0001464 mir-4510 miRBase:MIPF0001467 mir-4429 miRBase:MIPF0001474 mir-4716 miRBase:MIPF0001476 mir-3617 miRBase:MIPF0001477 mir-1273c miRBase:MIPF0001481 mir-3188 miRBase:MIPF0001488 mir-3937 miRBase:MIPF0001500 mir-3117 miRBase:MIPF0001506 mir-4654 miRBase:MIPF0001507 mir-4504 miRBase:MIPF0001508 mir-3132 miRBase:MIPF0001509 mir-6089 miRBase:MIPF0001510 mir-4803 miRBase:MIPF0001511 mir-4515 miRBase:MIPF0001512 mir-3664 miRBase:MIPF0001518 mir-3612 miRBase:MIPF0001519 mir-3938 miRBase:MIPF0001520 mir-4738 miRBase:MIPF0001521 mir-2278 miRBase:MIPF0001522 mir-3126 miRBase:MIPF0001525 mir-3923 miRBase:MIPF0001527 mir-4791 miRBase:MIPF0001529 mir-3661 miRBase:MIPF0001530 mir-3615 miRBase:MIPF0001540 mir-4526 miRBase:MIPF0001545 mir-4782 miRBase:MIPF0001546 mir-4421 miRBase:MIPF0001548 mir-3122 miRBase:MIPF0001549 mir-4672 miRBase:MIPF0001551 mir-4742 miRBase:MIPF0001552 mir-629 miRBase:MIPF0001555 mir-3607 miRBase:MIPF0001566 mir-3174 miRBase:MIPF0001569 mir-4788 miRBase:MIPF0001573 mir-4798 miRBase:MIPF0001574 mir-3136 miRBase:MIPF0001575 mir-4774 miRBase:MIPF0001578 mir-4451 miRBase:MIPF0001582 mir-3934 miRBase:MIPF0001584 mir-4637 miRBase:MIPF0001586 mir-4423 miRBase:MIPF0001587 mir-3192 miRBase:MIPF0001597 mir-3940 miRBase:MIPF0001599 mir-3912 miRBase:MIPF0001601 mir-2392 miRBase:MIPF0001614 mir-3140 miRBase:MIPF0001615 mir-3690 miRBase:MIPF0001618 mir-4488 miRBase:MIPF0001623 mir-3146 miRBase:MIPF0001626 mir-4428 miRBase:MIPF0001630 mir-1976 miRBase:MIPF0001633 mir-3165 miRBase:MIPF0001635 mir-3170 miRBase:MIPF0001637 mir-3605 miRBase:MIPF0001639 mir-4427 miRBase:MIPF0001640 mir-1199 miRBase:MIPF0001659 mir-6516 miRBase:MIPF0001672 mir-6770 miRBase:MIPF0001692 mir-7973 miRBase:MIPF0001693 mir-6859 miRBase:MIPF0001698 mir-6715 miRBase:MIPF0001708 mir-3618 miRBase:MIPF0001710 mir-6794 miRBase:MIPF0001726 mir-6827 miRBase:MIPF0001747 mir-5697 miRBase:MIPF0001748 mir-4703 miRBase:MIPF0001759 mir-4766 miRBase:MIPF0001764 mir-1911 miRBase:MIPF0001787 mir-8071 miRBase:MIPF0001799 mir-6505 miRBase:MIPF0001805 mir-6790 miRBase:MIPF0001811 mir-1243 miRBase:MIPF0001821 mir-3167 miRBase:MIPF0001823 mir-7641 miRBase:MIPF0001825 mir-4433 miRBase:MIPF0001826 mir-4677 miRBase:MIPF0001848 mir-6862 miRBase:MIPF0001855 mir-6724 miRBase:MIPF0001920 mir-3118 miRBase:MIPF0001928 mir-3149 miRBase:MIPF0001935 mir-1277 miRBase:MIPF0001937 mir-3648 miRBase:MIPF0001984 mir-4680 miRBase:MIPF0001988 mir-4657 miRBase:MIPF0002009 mir-8069 miRBase:MIPF0002050 mir-3687 miRBase:MIPF0002051 mir-4449 miRBase:MIPF0002103 mir-4523 miRBase:MIPF0002104 hsa-miR-125b-5p miRBase:MIMAT0000423 hsa-miR-125b-1-3p miRBase:MIMAT0004592 hsa-miR-125b-2-3p miRBase:MIMAT0004603 non-coding RNA A non-coding RNA (ncRNA) is an RNA molecule that is not translated into a protein. Alan Ruttenberg WEB:https://en.wikipedia.org/w/index.php?title=Non-coding_RNA&oldid=688555892#Non-coding RNA ncRNA genetic non-coding RNA A genetic non-coding RNA is a non-coding RNA that is created by transcription in a cell Alan Ruttenberg TODO: Add axiom linking GO transcription synthesized non-coding RNA Alan Ruttenberg TODO: Add axiom relating to OBI planned process and anything else from OBI that is relevant a RNA that is manufactured in a planned process long non-coding RNA Alan Ruttenberg Long non-coding RNAs (long ncRNAs, lncRNA) are non-protein coding transcripts longer than 200 nucleotides. Should requested and then imported from ChEBI This somewhat arbitrary limit distinguishes long ncRNAs from small regulatory RNAs such as microRNAs (miRNAs), short interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and other short RNAs WEB:https://en.wikipedia.org/w/index.php?title=Long_non-coding_RNA&oldid=687562040#Long non-coding RNA lncRNA small interfering RNA Alan Ruttenberg Should requested and then imported from ChEBI WEB:https://en.wikipedia.org/w/index.php?title=Special:CiteThisPage&page=Small_interfering_RNA&id=685334024#Small_interfering_RNA siRNA small interfering RNA (siRNA) is a class of double-stranded RNA molecules, 20-25 base pairs in length. siRNA plays many roles, but it is most notable in the RNA interference (RNAi) pathway, where it interferes with thes expression of specific genes with complementary nucleotide sequences. processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material organism 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') GROUP: OBI Biomaterial Branch A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. WEB: http://en.wikipedia.org/wiki/Organism animal fungus organism plant virus cultured cell population A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. PERSON:Matthew Brush PERSON:Matthew Brush cultured cell population 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. cell culture sample protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA. amino acid chain A molecular entity that is a polymer of amino acids residues linked by peptide bonds. region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. sequence sequence_secondary_structure A folded sequence. sequence secondary structure linkage_group A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned. http://en.wikipedia.org/wiki/Linkage_group linkage group nuclear_gene A gene from nuclear sequence. http://en.wikipedia.org/wiki/Nuclear_gene nuclear gene mt_gene A gene located in mitochondrial sequence. http://en.wikipedia.org/wiki/Mitochondrial_gene mitochondrial gene mt gene kinetoplast_gene A gene located in kinetoplast sequence. kinetoplast gene plastid_gene A gene from plastid sequence. plastid gene apicoplast_gene A gene from apicoplast sequence. apicoplast gene ct_gene A gene from chloroplast sequence. chloroplast gene ct gene chromoplast_gene A gene from chromoplast_sequence. chromoplast gene cyanelle_gene A gene from cyanelle sequence. cyanelle gene leucoplast_gene A plastid gene from leucoplast sequence. leucoplast gene proplastid_gene A gene from proplastid sequence. proplastid gene nucleomorph_gene A gene from nucleomorph sequence. nucleomorph gene plasmid_gene A gene from plasmid sequence. plasmid gene proviral_gene A gene from proviral sequence. proviral gene endogenous_retroviral_gene A proviral gene with origin endogenous retrovirus. endogenous retroviral gene transposable_element A transposon or insertion sequence. An element that can insert in a variety of DNA sequences. http://en.wikipedia.org/wiki/Transposable_element transposable element transposon polypeptide A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. http://en.wikipedia.org/wiki/Polypeptide protein mRNA_with_frameshift An mRNA with a frameshift. frameshifted mRNA mRNA with frameshift sequence_feature Any extent of continuous biological sequence. located_sequence_feature sequence feature transposable_element_gene A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast. transposable element gene silenced_gene A gene that is silenced. silenced gene gene_silenced_by_DNA_modification A gene that is silenced by DNA modification. gene silenced by DNA modification gene_silenced_by_DNA_methylation A gene that is silenced by DNA methylation. gene silenced by DNA methylation methylation-silenced gene gene_rearranged_at_DNA_level An epigenetically modified gene, rearranged at the DNA level. gene rearranged at DNA level deletion The point at which one or more contiguous nucleotides were excised. deleted_sequence http://en.wikipedia.org/wiki/Nucleotide_deletion loinc:LA6692-3 nucleotide deletion nucleotide_deletion promoter A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. http://en.wikipedia.org/wiki/Promoter promoter sequence RNApol_I_promoter A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription. RNA polymerase A promoter RNApol I promoter pol I promoter polymerase I promoter RNApol_II_promoter A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription. RNA polymerase B promoter RNApol II promoter polymerase II promoter RNApol_III_promoter A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription. RNA polymerase C promoter RNApol III promoter pol III promoter polymerase III promoter primary_transcript A transcript that in its initial state requires modification to be functional. http://en.wikipedia.org/wiki/Primary_transcript precursor RNA primary transcript mature_transcript A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified. http://en.wikipedia.org/wiki/Mature_transcript mature transcript mRNA Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. http://en.wikipedia.org/wiki/MRNA messenger RNA flanking_region The sequences extending on either side of a specific region. flanking region miRNA Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. http://en.wikipedia.org/wiki/MiRNA http://en.wikipedia.org/wiki/StRNA micro RNA microRNA small temporal RNA stRNA Removed axiom 'derives_from some miRNA_primary_transcript' pending review of status of SO terms. Changed relation of small regulatory ncRNA (superclass) into is about relationship engineered_gene A gene that is engineered. engineered gene engineered_foreign_gene A gene that is engineered and foreign. engineered foreign gene mRNA_with_minus_1_frameshift An mRNA with a minus 1 frameshift. mRNA with minus 1 frameshift engineered_foreign_transposable_element_gene A transposable_element that is engineered and foreign. engineered foreign transposable element gene foreign_gene A gene that is foreign. foreign gene fusion_gene A gene that is a fusion. fusion gene http://en.wikipedia.org/wiki/Fusion_gene engineered_fusion_gene A fusion gene that is engineered. engineered fusion gene origin_of_replication The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies. http://en.wikipedia.org/wiki/Origin_of_replication ori origin of replication recombination_feature recombination feature CpG_island CG island CpG island Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes. http://en.wikipedia.org/wiki/CpG_island mRNA_with_plus_1_frameshift An mRNA with a plus 1 frameshift. mRNA with plus 1 frameshift mRNA_with_plus_2_frameshift An mRNA with a plus 2 frameshift. mRNA with plus 2 frameshift mRNA_with_minus_2_frameshift A mRNA with a minus 2 frameshift. mRNA with minus 2 frameshift pseudogene A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog). http://en.wikipedia.org/wiki/Pseudogene floxed_gene A transgene that is floxed. floxed gene transposable_element_flanking_region The region of sequence surrounding a transposable element. transposable element flanking region insertion_site The junction where an insertion occurred. insertion site transposable_element_insertion_site The junction in a genome where a transposable_element has inserted. transposable element insertion site small_regulatory_ncRNA A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression. small regulatory ncRNA recombinationally_inverted_gene A recombinationally rearranged gene by inversion. recombinationally inverted gene RNA_6S 6S RNA A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase. RNA 6S http://en.wikipedia.org/wiki/6S_RNA CsrB_RsmB_RNA An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family. CsrB RsmB RNA CsrB-RsmB RNA DsrA_RNA DsrA RNA DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation. http://en.wikipedia.org/wiki/DsrA_RNA OxyS_RNA A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages. OxyS RNA http://en.wikipedia.org/wiki/OxyS_RNA RprA_RNA RprA RNA Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential. http://en.wikipedia.org/wiki/RprA_RNA RRE_RNA RRE RNA The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins. spot_42_RNA A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels. http://en.wikipedia.org/wiki/Spot_42_RNA spot-42 RNA binding_site A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. binding_or_interaction_site http://en.wikipedia.org/wiki/Binding_site gene_with_polyadenylated_mRNA A gene that encodes a polyadenylated mRNA. gene with polyadenylated mRNA gene_with_mRNA_with_frameshift A gene that encodes an mRNA with a frameshift. gene with mRNA with frameshift recombinationally_rearranged_gene A gene that is recombinationally rearranged. recombinationally rearranged gene gene_with_trans_spliced_transcript A gene with a transcript that is trans-spliced. gene with trans spliced transcript pseudogenic_region A non-functional descendant of a functional entity. pseudogenic region nc_primary_transcript A primary transcript that is never translated into a protein. nc primary transcript noncoding primary transcript gene_with_edited_transcript A gene that encodes a transcript that is edited. gene with edited transcript bidirectional_promoter An unregulated promoter that allows continuous expression. bidirectional promoter cap A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA. http://en.wikipedia.org/wiki/5%27_cap tmRNA A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes. http://en.wikipedia.org/wiki/TmRNA intergenic_region A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome. http://en.wikipedia.org/wiki/Intergenic_region intergenic region oligo_U_tail The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602). oligo U tail polyA_sequence Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs. polyA sequence bacterial_RNApol_promoter A DNA sequence to which bacterial RNA polymerase binds, to begin transcription. bacterial RNApol promoter RNApol_III_promoter_type_1 RNApol III promoter type 1 RNApol_III_promoter_type_2 RNApol III promoter type 2 RNApol_III_promoter_type_3 RNApol III promoter type 3 insulator A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression. http://en.wikipedia.org/wiki/Insulator_(genetics) insulator element monocistronic_mRNA An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap. http://en.wikipedia.org/wiki/Monocistronic_mRNA monocistronic mRNA monocistronic processed transcript polycistronic_mRNA An mRNA that encodes multiple proteins from at least two non-overlapping regions. http://en.wikipedia.org/wiki/Polycistronic_mRNA polycistronic mRNA miRNA_primary_transcript A primary transcript encoding a micro RNA. miRNA primary transcript micro RNA primary transcript small temporal RNA primary transcript stRNA primary transcript stRNA_primary_transcript maxicircle_gene A mitochondrial gene located in a maxicircle. maxi-circle gene maxicircle gene ncRNA An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. http://en.wikipedia.org/wiki/NcRNA noncoding RNA repeat_region A region of sequence containing one or more repeat units. repeat region insertion The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. insertion loinc:LA6687-3 nucleotide insertion nucleotide_insertion transcript An RNA synthesized on a DNA or RNA template by an RNA polymerase. http://en.wikipedia.org/wiki/RNA gene_with_polycistronic_transcript A gene that encodes a polycistronic transcript. gene with polycistronic transcript gene_with_dicistronic_transcript A gene that encodes a dicistronic transcript. gene with dicistronic transcript gene_with_recoded_mRNA A gene that encodes an mRNA that is recoded. gene with recoded mRNA gene_with_stop_codon_read_through A gene that encodes a transcript with stop codon readthrough. gene with stop codon read through gene_with_stop_codon_redefined_as_pyrrolysine A gene encoding an mRNA that has the stop codon redefined as pyrrolysine. gene with stop codon redefined as pyrrolysine junction A sequence_feature with an extent of zero. boundary breakpoint gene A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. http://en.wikipedia.org/wiki/Gene gene_with_stop_codon_redefined_as_selenocysteine A gene encoding an mRNA that has the stop codon redefined as selenocysteine. gene with stop codon redefined as selenocysteine gene_with_mRNA_recoded_by_translational_bypass A gene with mRNA recoded by translational bypass. gene with mRNA recoded by translational bypass gene_with_transcript_with_translational_frameshift A gene encoding a transcript that has a translational frameshift. gene with transcript with translational frameshift dicistronic_mRNA An mRNA that has the quality dicistronic. dicistronic mRNA foreign_transposable_element A transposable element that is foreign. foreign transposable element gene_with_dicistronic_primary_transcript A gene that encodes a dicistronic primary transcript. gene with dicistronic primary transcript gene_with_dicistronic_mRNA A gene that encodes a polycistronic mRNA. gene with dicistronic mRNA gene with dicistronic processed transcript repeat_unit The simplest repeated component of a repeat region. A single repeat. http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html repeat unit CRM A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. TF module cis regulatory module transcription factor module exemplar_mRNA An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group. exemplar mRNA QTL A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. quantitative trait locus natural_transposable_element TE that exists (or existed) in nature. natural transposable element engineered_transposable_element TE that has been modified by manipulations in vitro. engineered transposable element rescue_gene A gene that rescues. rescue gene wild_type_rescue_gene A gene that rescues. wild type rescue gene chromosome_part A region of a chromosome. chromosome part gene_member_region A region of a gene. gene member region transcript_region A region of a transcript. transcript region polypeptide_region Biological sequence region that can be assigned to a specific subsequence of a polypeptide. gene_component_region gene component region capped_mRNA An mRNA that is capped. capped mRNA polyadenylated_mRNA An mRNA that is polyadenylated. polyadenylated mRNA trans_spliced_mRNA An mRNA that is trans-spliced. trans-spliced mRNA maternally_imprinted_gene A gene that is maternally_imprinted. maternally imprinted gene paternally_imprinted_gene A gene that is paternally imprinted. paternally imprinted gene post_translationally_regulated_gene A gene that is post translationally regulated. post translationally regulated gene negatively_autoregulated_gene A gene that is negatively autoreguated. negatively autoregulated gene positively_autoregulated_gene A gene that is positively autoregulated. positively autoregulated gene translationally_regulated_gene A gene that is translationally regulated. translationally regulated gene allelically_excluded_gene A gene that is allelically_excluded. allelically excluded gene epigenetically_modified_gene A gene that is epigenetically modified. epigenetically modified gene transgene A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another. http://en.wikipedia.org/wiki/Transgene edited_mRNA An mRNA that is edited. edited mRNA recombinationally_rearranged_vertebrate_immune_system_gene A recombinationally rearranged gene of the vertebrate immune system. recombinationally rearranged vertebrate immune system gene minicircle_gene minicircle gene consensus_mRNA consensus mRNA predicted_gene predicted gene mobile_genetic_element A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome. MGE http://en.wikipedia.org/wiki/Mobile_genetic_element mobile genetic element transcriptional_cis_regulatory_region A regulatory_region that modulates the transcription of a gene or genes. transcription-control region transcriptional cis regulatory region promoter_targeting_sequence A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter. promoter targeting sequence RNA_polymerase_promoter A region (DNA) to which RNA polymerase binds, to begin transcription. RNA polymerase promoter Phage_RNA_Polymerase_Promoter A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription. Phage RNA Polymerase Promoter SP6_RNA_Polymerase_Promoter A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription. SP6 RNA Polymerase Promoter T3_RNA_Polymerase_Promoter A DNA sequence to which the T3 RNA polymerase binds, to begin transcription. T3 RNA Polymerase Promoter T7_RNA_Polymerase_Promoter A region (DNA) to which the T7 RNA polymerase binds, to begin transcription. T7 RNA Polymerase Promoter protein_coding_gene protein coding gene retrogene gene_silenced_by_RNA_interference A gene that is silenced by RNA interference. RNA interference silenced gene RNAi silenced gene gene silenced by RNA interference gene_silenced_by_histone_modification A gene that is silenced by histone modification. gene silenced by histone modification gene_silenced_by_histone_methylation A gene that is silenced by histone methylation. gene silenced by histone methylation gene_silenced_by_histone_deacetylation A gene that is silenced by histone deacetylation. gene silenced by histone deacetylation replicon A region containing at least one unique origin of replication and a unique termination site. http://en.wikipedia.org/wiki/Replicon_(genetics) base A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. http://en.wikipedia.org/wiki/Nucleobase amino_acid A sequence feature that corresponds to a single amino acid residue in a polypeptide. amino acid http://en.wikipedia.org/wiki/Amino_acid ncRNA_gene ncRNA gen ncRNA gene gRNA_gene gRNA gene miRNA_gene miRNA gene stRNA gene stRNA_gene scRNA_gene scRNA gene snoRNA_gene snoRNA gene snRNA_gene snRNA gene SRP_RNA_gene SRP RNA gene tmRNA_gene tmRNA gene tRNA_gene tRNA gene biological_region A region defined by its disposition to be involved in a biological process. biological region topologically_defined_region A region that is defined according to its relations with other regions within the same sequence. topologically defined region cryptic_gene A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning. cryptic gene rRNA_gene A gene that encodes for ribosomal RNA. rDNA rRNA gene piRNA_gene A gene that encodes for an piwi associated RNA. piRNA gene RNase_P_RNA_gene A gene that encodes an RNase P RNA. RNase P RNA gene RNase_MRP_RNA_gene A gene that encodes a RNase_MRP_RNA. lincRNA_gene A gene that encodes large intervening non-coding RNA. lincRNA gene telomerase_RNA_gene A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase. TERC Telomerase RNA component http:http://en.wikipedia.org/wiki/Telomerase_RNA_component telomerase RNA gene genetic_marker A measurable sequence feature that varies within a population. RNApol_II_core_promoter RNApol II core promoter The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes. bacterial_RNApol_promoter_sigma_70 bacterial RNA polymerase promoter sigma 70 bacterial_RNApol_promoter_sigma54 bacterial RNA polymerase promoter sigma54 transcription_regulatory_region A regulatory region that is involved in the control of the process of transcription. transcription regulatory region sequence_motif A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance. http://en.wikipedia.org/wiki/Sequence_motif restriction_enzyme_recognition_site The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site. restriction endonuclease recognition site restriction enzyme recognition site restriction_enzyme_single_strand_overhang A terminal region of DNA sequence where the end of the region is not blunt ended. single strand overhang ISRE An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding. interferon stimulated response element epigenetically_modified_region A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence. gene_with_non_canonical_start_codon A gene with a start codon other than AUG. gene with non canonical start codon gene_with_start_codon_CUG A gene with a translational start codon of CUG. gene with start codon CUG open_chromatin_region A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA. open chromatin region candidate_gene A gene suspected of being involved in the expression of a trait. candidate gene target gene positional_candidate_gene A candidate gene whose association with a trait is based on the gene's location on a chromosome. positional candidate gene functional_candidate_gene A candidate gene whose function has something in common biologically with the trait under investigation. functional candidate gene functional target gene rearrangement_region A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome. rearrangement region transposable_element_CDS A CDS that is part of a transposable element. transposable element CDS transposable_element_pseudogene A pseudogene contained within a transposable element. transposable element pseudogene bacterial_RNApol_promoter_sigma_ecf A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation. bacterial RNApol promoter sigma ecf regulatory_region A region of sequence that is involved in the control of a biological process. http://en.wikipedia.org/wiki/Regulatory_region regulatory region gene_cassette A gene that can be substituted for a related gene at a different site in the genome. gene cassette http://en.wikipedia.org/wiki/Gene_cassette gene_group A collection of related genes. gene group substitution A sequence alteration where the length of the change in the variant is the same as that of the reference. loinc:LA6690-7 inversion A continuous nucleotide sequence is inverted in the same position. inversion loinc:LA6689-9 cryptogene A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence. recoded_mRNA The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals. recoded mRNA mRNA_recoded_by_translational_bypass A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon. mRNA recoded by translational bypass mRNA_recoded_by_codon_redefinition A recoded_mRNA that was modified by an alteration of codon meaning. mRNA recoded by codon redefinition retron Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes. anatomical structure AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. TAO:0000037 TGMA:0001823 VHOG:0001759 WBbt:0000100 XAO:0003000 ZFA:0000037 biological structure connected biological structure organ Anatomical structure that performs a specific function or group of functions [WP]. CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA UMLS:C0178784 WBbt:0003760 material anatomical entity AAO:0010264 AEO:0000006 Anatomical entity that has mass. BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 tissue AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. TAO:0001477 TGMA:0001844 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue portion of tissue tissue portion example to be eventually removed failed exploratory term Person:Alan Ruttenberg The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. organizational term term created to ease viewing/sort terms for development purpose, and will not be included in a release ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. core Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. universal A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf Alan Ruttenberg Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. defined class "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal Alan Ruttenberg named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. Alan Ruttenberg named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions to be replaced with external ontology term Alan Ruttenberg Terms with this status should eventually replaced with a term from another ontology. group:OBI requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI Person:Alan Ruttenberg To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])